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.929.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: 0.03u 0.00s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 23.79
//
[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:

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:

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:

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:

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