Alignments for a candidate for putA in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for putA in Paraburkholderia bryophila 376MFSha3.1

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate H281DRAFT_02404 H281DRAFT_02404 L-proline dehydrogenase /delta-1-pyrroline-5-carboxylate dehydrogenase

Query= reanno::Cup4G11:RR42_RS20125
         (1333 letters)



>FitnessBrowser__Burk376:H281DRAFT_02404
          Length = 1312

 Score = 1759 bits (4557), Expect = 0.0
 Identities = 917/1345 (68%), Positives = 1065/1345 (79%), Gaps = 45/1345 (3%)

Query: 1    MATTTLGVKLDDASRERLKRVAQSIDRTPHWLIKQAIFTYLEQVERGNIPHETSAAGTGS 60
            MA+TTLGVK+DD  R RL+  A  ++RTPHWLIKQAIF YLE++E+G +P E S      
Sbjct: 1    MASTTLGVKVDDLLRSRLRDAATRLERTPHWLIKQAIFAYLEKIEQGQLPPELS------ 54

Query: 61   EGAADGADAFDGAA----SDGAIQPFLEFAQSVQPQSVLRAAITAAYRRPESECVPVLLE 116
             G A  AD  DGA+     DGA  PFL+FAQ+VQPQSVLRAAITAAYRRPE ECVP LL 
Sbjct: 55   -GVAGSADMADGASVEPDEDGAAHPFLDFAQNVQPQSVLRAAITAAYRRPEPECVPFLLG 113

Query: 117  QARLPHQQAEAALAMARTLATRLRERKVGTGREGLVQGLIQEFSLSSQEGVALMCLAEAL 176
            QARLP   A    A+A  L   LR +  G G    V+GLI EFSLSSQEGVALMCLAEAL
Sbjct: 114  QARLPANLAGDVQALAAKLVETLRGKSKGGG----VEGLIHEFSLSSQEGVALMCLAEAL 169

Query: 177  LRIPDKATRDALIRDKISGANWQSHLGQSPSVFVNAATWGLLFTGKLVATHTEAGLSKAL 236
            LRIPD+ATRDALIRDKIS  +W+SH+GQ+PS+FVNAATWGL+ TGKLV T++E  LS AL
Sbjct: 170  LRIPDRATRDALIRDKISKGDWKSHVGQAPSLFVNAATWGLMITGKLVTTNSETNLSSAL 229

Query: 237  TRIIGKGGEPLIRKGVDMAMRLMGEQFVTGETISEALANARKYEAEGFRYSYDMLGEAAM 296
            TR+IGKGGEPLIRKGVDMAMRLMGEQFVTGE ISEALAN+RKYEA GFRYSYDMLGEAA 
Sbjct: 230  TRLIGKGGEPLIRKGVDMAMRLMGEQFVTGENISEALANSRKYEARGFRYSYDMLGEAAT 289

Query: 297  TEADAQRYLASYEQAINAIGQASRGRGIYEGPGISIKLSALHPRYSRAQHERVIGELYGR 356
            TEADAQRY ASYEQAI+AIG+A+ GRGIYEGPGISIKLSALHPRYSR+Q ER + EL  R
Sbjct: 290  TEADAQRYYASYEQAIHAIGKAAGGRGIYEGPGISIKLSALHPRYSRSQQERTMSELLPR 349

Query: 357  LKSLTLLARQYDIGINIDAEEADRLEISLDLLERLCFEPELAGWNGIGFVVQGYQKRCPF 416
            ++SL +LAR+YDIG+NIDAEEADRLEISLDLLE LCF+PELAGWNGIGFVVQ YQKRCPF
Sbjct: 350  VRSLAILARRYDIGLNIDAEEADRLEISLDLLEALCFDPELAGWNGIGFVVQAYQKRCPF 409

Query: 417  VIDYLIDLARRSRHRLMIRLVKGAYWDSEIKRAQVDGLEGYPVYTRKVYTDVSYVACARK 476
            VI+Y++DLARRSRHR+M+RLVKGAYWD+EIKRAQVDGLEGYPVYTRK+YTDVSY+ACA+K
Sbjct: 410  VIEYIVDLARRSRHRIMVRLVKGAYWDTEIKRAQVDGLEGYPVYTRKIYTDVSYLACAKK 469

Query: 477  LLSVPDVIYPQFATHNAHTLAAIYQIAGHNYYPGQYEFQCLHGMGEPLYDQVVGPLADGK 536
            LL  PD +YPQFATHNAHTL+AIY +AG+NYYPGQYEFQCLHGMGEPLY++V GPL+ GK
Sbjct: 470  LLGAPDAVYPQFATHNAHTLSAIYHLAGNNYYPGQYEFQCLHGMGEPLYEEVTGPLSAGK 529

Query: 537  FNRPCRIYAPVGTHETLLAYLVRRLLENGANTSFVNRIADDTISLDELVADPVAVVEQMH 596
             NRPCR+YAPVGTHETLLAYLVRRLLENGANTSFVNRIAD+ +++ +L+ADPV    ++ 
Sbjct: 530  LNRPCRVYAPVGTHETLLAYLVRRLLENGANTSFVNRIADENVAIQDLIADPVEEASKI- 588

Query: 597  ADEGALGLPHPRIAQPRTLYGESRANSAGIDLSNEHRLASLSSALLAGTSEAVSAVPLLG 656
                 LG PH +I  PR LYG  R NS G+DLSNEHRLASLSSALLA  +    A P+L 
Sbjct: 589  ---VPLGAPHAKIPLPRNLYGAERLNSMGLDLSNEHRLASLSSALLASANHPWRAAPMLA 645

Query: 657  TEAAAGEDVNQPAPVRNPSDQRDVVGHVTEASMAEVEAALQAAVNAAPIWQATPADVRAA 716
             +      +     VRNP+D RD+VG V EAS   V AAL  AV AAPIWQATP + RA 
Sbjct: 646  DDQIV---LGNARDVRNPADHRDLVGTVVEASAEHVSAALAHAVAAAPIWQATPVEARAD 702

Query: 717  ALERAAELMEAQMQSLMGIIVREAGKTFSNAIAEVREAVDFLRYYAAQVRETFSSDTHRP 776
             L RAA+L+EAQM +LMG++VREAGK+ +NA++E+REA+DFLRYY+ Q+R  FS+DTHRP
Sbjct: 703  CLARAADLLEAQMHTLMGLVVREAGKSLANAVSEIREAIDFLRYYSTQIRSEFSNDTHRP 762

Query: 777  LGPVVCISPWNFPLAIFTGQVAAALAAGNTVLAKPAEQTPLIAAQAVRLLREAGVPAGAV 836
            LGPVVCISPWNFPLAIF GQVAAALAAGNTVLAKPAEQTPLIAAQAVR+LREAGVPAGAV
Sbjct: 763  LGPVVCISPWNFPLAIFMGQVAAALAAGNTVLAKPAEQTPLIAAQAVRILREAGVPAGAV 822

Query: 837  QLLPGRGETVGAALVGDARVKGVMFTGSTEVARLLQRSVAGRLDAAGRPVPLIAETGGQN 896
            QLLPG GETVGAALV D R + VMFTGSTEVARL+ ++++GRLD  G+P+PLIAETGGQN
Sbjct: 823  QLLPGDGETVGAALVADPRTRAVMFTGSTEVARLINKTLSGRLDPEGKPIPLIAETGGQN 882

Query: 897  AMIVDSSALAEQVVGDVVNSAFDSAGQRCSALRVLCLQEEVADRVLEMLKGAMDELTMGN 956
            AMIVDSSALAEQVV DV+ S+FDSAGQRCSALRVLCLQ++VADR LEML GAM ELT+GN
Sbjct: 883  AMIVDSSALAEQVVADVMQSSFDSAGQRCSALRVLCLQDDVADRTLEMLTGAMRELTVGN 942

Query: 957  PDRLSTDVGPVIDEEARGNIVRHIDAMRAKGRRVHQADPNGALSAACRNGTFVSPTLIEL 1016
            PDRLSTDVGPVID +A+  I  HI AMR KGR+V Q      +   C  GTFV PTLIEL
Sbjct: 943  PDRLSTDVGPVIDVDAKRGIDAHIAAMREKGRKVEQL----PMPEGCAQGTFVPPTLIEL 998

Query: 1017 DSIEELQREVFGPVLHVVRYPRAGLDTLLAQINGTGYGLTMGIHTRIDETIEHIVERAEV 1076
            DSI+EL+REVFGPVLHVVRY R+ LD LL QI  TGYGLT+GIHTRIDETI H++ RA V
Sbjct: 999  DSIDELKREVFGPVLHVVRYRRSQLDQLLEQIRTTGYGLTLGIHTRIDETIAHVISRAHV 1058

Query: 1077 GNLYVNRNIVGAVVGVQPFGGEGLSGTGPKAGGPLYLHRLLSVCPLDAVARVVRASDT-V 1135
            GN+YVNRN++GAVVGVQPFGGEGLSGTGPKAGG LYL RLL+  P      + +A    V
Sbjct: 1059 GNIYVNRNVIGAVVGVQPFGGEGLSGTGPKAGGALYLQRLLATRPAGLPKSLAQALIVDV 1118

Query: 1136 GGADETGPVRRTLTETLATLKEW--AQRESAALPGLVAACERFAAASAAGLSVTLPGPTG 1193
              A E G      +  L  L++W  A+RE    P L A C+ + +   AG +  L GPTG
Sbjct: 1119 PQAAEKGD---NPSAALTALRDWLIAERE----PQLAARCDGYLSHMPAGATAVLSGPTG 1171

Query: 1194 ERNTYTLLPRAAVLCLAQQETDLAVQLAAVLAAGSQAVWVESPMARALFARLPKAVQSRV 1253
            ERNTYTL  R  VLC+A   +    Q AAVLA G++A++ E      L  +LP +++S  
Sbjct: 1172 ERNTYTLGARGTVLCIASTASGARAQFAAVLATGNRALF-EGAAGEQLVTQLPASLKSYA 1230

Query: 1254 RLVADWSAGDTGFDAVLHHGDSDQLRAVCEQLATRPGPIISVQGLA-----HGEPNIAIE 1308
             +  +    +T FDAVL  GDSD+L  + +++A RPGPI+SVQG+A      G+ + A+E
Sbjct: 1231 SVRKN---AETPFDAVLFEGDSDELLTLVKEVAKRPGPIVSVQGVASRALESGDEDYALE 1287

Query: 1309 RLLIERSLSVNTAAAGGNASLMTIG 1333
            RLL ERS+SVNTAAAGGNA+LMTIG
Sbjct: 1288 RLLTERSVSVNTAAAGGNANLMTIG 1312


Lambda     K      H
   0.318    0.133    0.383 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 4000
Number of extensions: 153
Number of successful extensions: 10
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 1333
Length of database: 1312
Length adjustment: 49
Effective length of query: 1284
Effective length of database: 1263
Effective search space:  1621692
Effective search space used:  1621692
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 59 (27.3 bits)

Align candidate H281DRAFT_02404 H281DRAFT_02404 (L-proline dehydrogenase /delta-1-pyrroline-5-carboxylate dehydrogenase)
to HMM TIGR01238 (delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.2.1.88))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR01238.hmm
# target sequence database:        /tmp/gapView.8550.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01238  [M=500]
Accession:   TIGR01238
Description: D1pyr5carbox3: delta-1-pyrroline-5-carboxylate dehydrogenase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                    Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
   2.9e-243  793.8   0.9     4e-243  793.3   0.9    1.2  1  lcl|FitnessBrowser__Burk376:H281DRAFT_02404  H281DRAFT_02404 L-proline dehydr


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_02404  H281DRAFT_02404 L-proline dehydrogenase /delta-1-pyrroline-5-carboxylate
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  793.3   0.9    4e-243    4e-243       1     499 [.     603    1102 ..     603    1103 .. 0.99

  Alignments for each domain:
  == domain 1  score: 793.3 bits;  conditional E-value: 4e-243
                                    TIGR01238    1 dlygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdi 64  
                                                   +lyg  r ns+G+dl+ne++l+sl++ ll++a++ ++aap++++++   g+a+ v+npad++d+
  lcl|FitnessBrowser__Burk376:H281DRAFT_02404  603 NLYGAERLNSMGLDLSNEHRLASLSSALLASANHPWRAAPMLADDQIVLGNARDVRNPADHRDL 666 
                                                   59************************************************************** PP

                                    TIGR01238   65 vGqvseadaaevqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktl 128 
                                                   vG+v ea+a++v++a+  avaa+++w+at+ + ra +l r+adlle +m +l++l+vreaGk+l
  lcl|FitnessBrowser__Burk376:H281DRAFT_02404  667 VGTVVEASAEHVSAALAHAVAAAPIWQATPVEARADCLARAADLLEAQMHTLMGLVVREAGKSL 730 
                                                   **************************************************************** PP

                                    TIGR01238  129 snaiaevreavdflryyakqvedvldeesakalGavvcispwnfplaiftGqiaaalaaGntvi 192 
                                                    na++e+rea+dflryy+ q++ +++++++++lG+vvcispwnfplaif+Gq+aaalaaGntv+
  lcl|FitnessBrowser__Burk376:H281DRAFT_02404  731 ANAVSEIREAIDFLRYYSTQIRSEFSNDTHRPLGPVVCISPWNFPLAIFMGQVAAALAAGNTVL 794 
                                                   **************************************************************** PP

                                    TIGR01238  193 akpaeqtsliaaravellqeaGvpagviqllpGrGedvGaaltsderiaGviftGstevarlin 256 
                                                   akpaeqt+liaa+av +l+eaGvpag++qllpG Ge+vGaal +d+r + v+ftGstevarlin
  lcl|FitnessBrowser__Burk376:H281DRAFT_02404  795 AKPAEQTPLIAAQAVRILREAGVPAGAVQLLPGDGETVGAALVADPRTRAVMFTGSTEVARLIN 858 
                                                   **************************************************************** PP

                                    TIGR01238  257 kalakredap...vpliaetGGqnamivdstalaeqvvadvlasafdsaGqrcsalrvlcvqed 317 
                                                   k+l+ r d++   +pliaetGGqnamivds+alaeqvvadv++s+fdsaGqrcsalrvlc+q+d
  lcl|FitnessBrowser__Burk376:H281DRAFT_02404  859 KTLSGRLDPEgkpIPLIAETGGQNAMIVDSSALAEQVVADVMQSSFDSAGQRCSALRVLCLQDD 922 
                                                   *******987777*************************************************** PP

                                    TIGR01238  318 vadrvltlikGamdelkvgkpirlttdvGpvidaeakqnllahiekmkakakkvaqvkleddve 381 
                                                   vadr+l+++ Gam el vg+p rl tdvGpvid +ak+ + ahi +m++k++kv q+ + +   
  lcl|FitnessBrowser__Burk376:H281DRAFT_02404  923 VADRTLEMLTGAMRELTVGNPDRLSTDVGPVIDVDAKRGIDAHIAAMREKGRKVEQLPMPE--G 984 
                                                   **********************************************************999..9 PP

                                    TIGR01238  382 sekgtfvaptlfelddldelkkevfGpvlhvvrykadeldkvvdkinakGygltlGvhsrieet 445 
                                                   + +gtfv+ptl+eld++delk+evfGpvlhvvry++++ld+++++i ++GygltlG+h+ri+et
  lcl|FitnessBrowser__Burk376:H281DRAFT_02404  985 CAQGTFVPPTLIELDSIDELKREVFGPVLHVVRYRRSQLDQLLEQIRTTGYGLTLGIHTRIDET 1048
                                                   **************************************************************** PP

                                    TIGR01238  446 vrqiekrakvGnvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplylyrltrvr 499 
                                                   ++++ +ra+vGn+yvnrn++GavvGvqpfGGeGlsGtGpkaGG+lyl+rl+ +r
  lcl|FitnessBrowser__Burk376:H281DRAFT_02404 1049 IAHVISRAHVGNIYVNRNVIGAVVGVQPFGGEGLSGTGPKAGGALYLQRLLATR 1102
                                                   **************************************************9765 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (500 nodes)
Target sequences:                          1  (1312 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04
# Mc/sec: 15.46
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources