Alignments for a candidate for putA in Sinorhizobium fredii NGR234

GapMind for catabolism of small carbon sources

Alignments for a candidate for putA in Sinorhizobium fredii NGR234

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate YP_002826548.1 NGR_c20320 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase

Query= reanno::azobra:AZOBR_RS23695
         (1235 letters)



>NCBI__GCF_000018545.1:YP_002826548.1
          Length = 1230

 Score = 1580 bits (4092), Expect = 0.0
 Identities = 818/1229 (66%), Positives = 945/1229 (76%), Gaps = 6/1229 (0%)

Query: 8    PSAAPGEAAPFADFAPPIRPATELRAAITAAYRRPEPECLPFLFEQASLPPGVITAAAAT 67
            P + P  A PFA FAPPIR  + LR  ITAAYRRPE ECLP L E A L        A  
Sbjct: 5    PLSEPDTARPFAAFAPPIRQQSTLRQEITAAYRRPETECLPPLVEAARLTGATKAKVAVI 64

Query: 68   ARKLITALRAKPRGRGVEGLIHEYSLSSQEGMALMCLAEALLRIPDHATRDALIRDKIAG 127
            ARKLI ALRAK +G GVEGL+HEYSLSSQEG+ALMCLAEALLRIPD  TRDALIRDKIA 
Sbjct: 65   ARKLIEALRAKHKGTGVEGLVHEYSLSSQEGVALMCLAEALLRIPDTETRDALIRDKIAE 124

Query: 128  GDWQAHLGKGGSMFVNAATWGLLITGKLTSAGGEQALSSALTRLIARGGEPLIRRGVDFA 187
            GDW++HLG   SMFVNAATWGL++TGKLTS   +++L++AL+RLIAR GEP+IRRGVD A
Sbjct: 125  GDWKSHLGGTKSMFVNAATWGLVVTGKLTSTVNDRSLAAALSRLIARAGEPVIRRGVDMA 184

Query: 188  MRMMGEQFVTGQTIQEALTNARTMEAEGFRYSYDMLGEAALTAEDAARYYADYVNAIHAI 247
            MRMMGEQFVTG+TIQEA+  ++ +EA GFRYSYDMLGEAA TA DA RY+ DY NAIHAI
Sbjct: 185  MRMMGEQFVTGETIQEAIKRSKPLEARGFRYSYDMLGEAATTAADATRYFRDYENAIHAI 244

Query: 248  GTASAGRGVYEGPGISIKLSAIHPRYSRAQADRVMDELLPRVKALALLAKGYDIGLNIDA 307
            G AS GRGVYEGPGISIKLSA+HPRY+R Q +RV+ ELLP+VK LALLAK YDIGLNIDA
Sbjct: 245  GKASGGRGVYEGPGISIKLSALHPRYTRTQTERVVGELLPKVKQLALLAKRYDIGLNIDA 304

Query: 308  EEADRLELSLDLMESLCFDPDLAGWNGIGFVVQAYGKRCPYVIDFLIDLARRSGHRLMIR 367
            EEADRLELSLDL+E L  D DL GW+G+GFVVQAYGKRCP+V+D++IDLARRSG R+M+R
Sbjct: 305  EEADRLELSLDLLEELSLDKDLGGWDGLGFVVQAYGKRCPFVLDYVIDLARRSGRRIMLR 364

Query: 368  LVKGAYWDSEIKRAQLDGLPDFPVYTRKVYTDVSYVACARKLLAAPEAVFPQFATHNAQT 427
            LVKGAYWD+EIKRAQLDGL  FPVYTRKV+TDV+Y+ACARKLLAAP+A+FPQFATHNAQ+
Sbjct: 365  LVKGAYWDAEIKRAQLDGLEGFPVYTRKVHTDVAYIACARKLLAAPDAIFPQFATHNAQS 424

Query: 428  LATIYEMAGSDFQVGKYEFQCLHGMGEPLYKEVVGPLK--RPCRIYAPVGTHETLLAYLV 485
            LATIYE+AG DF+VGKYEFQCLHGMGEPLY EVVG  K  RPCRIYAPVGTHETLLAYLV
Sbjct: 425  LATIYELAGPDFEVGKYEFQCLHGMGEPLYDEVVGKAKLDRPCRIYAPVGTHETLLAYLV 484

Query: 486  RRLLENGANSSFVNRIADPAVPVDELVADPVAVARAIAPTGAPHALIALPRNLYAPERAN 545
            RRLLENGANSSFVNRI+D  V VDEL+ DPV V  A+   G PH  IALP +LY  ERAN
Sbjct: 485  RRLLENGANSSFVNRISDENVSVDELITDPVDVVEAMPVVGMPHDQIALPADLYGRERAN 544

Query: 546  SAGIDLSDETELARLSAALSASAEMTWTAAPLLADGERAGQAQPVRNPADRRDVVGSVTE 605
            S G+DLS+E  LA L++ L A+    W A PLLADG   G+ +PV NPAD  DVVGSVTE
Sbjct: 545  SKGLDLSNEDTLADLASRLQATVTQDWHATPLLADGSLEGKTRPVVNPADHNDVVGSVTE 604

Query: 606  ASEALVAEAFGHAVAAASAWAATPPEERAASLFRAADTMQERMPTLLGLIVREAGKSLPN 665
             +    +     A   A+ WAAT P ERA  L RAAD MQER+  L+ + +REAGKS  N
Sbjct: 605  LAVEDASRIARMAAEGAAQWAATSPAERADCLERAADLMQERLEVLMAIAMREAGKSAAN 664

Query: 666  AIAEVREAIDFLRYYGAQVRDRFDNATHRPLGPVVCISPWNFPLAIFSGQIAAALAAGNP 725
            A+ EVREAIDFLRYY  Q R      +H PLG V+CISPWNFPLAIF+GQ+AAAL AGN 
Sbjct: 665  AVGEVREAIDFLRYYAVQARKTL-GPSHAPLGAVLCISPWNFPLAIFTGQVAAALVAGNS 723

Query: 726  VLAKPAEETPLIAAEAVRILHAAGIPAGALQLLPGAGEVGAALVGHEAVRGVMFTGSTEV 785
            V+AKPA  TP+IA E+V+ILH AG+P GALQ +PG+G +GAALV      GVMFTGSTEV
Sbjct: 724  VMAKPAGVTPIIAFESVKILHEAGVPRGALQFIPGSGRLGAALVAAPETAGVMFTGSTEV 783

Query: 786  ARLIQRQLAGRLLPDGAPIPLIAETGGQNAMIVDSSALAEQVVGDVIASAFDSAGQRCSA 845
            AR IQ QLA RL   G PIPLIAETGGQN MIVDSSALAEQVV DVIASAFDSAGQRCSA
Sbjct: 784  ARQIQAQLAERLSASGKPIPLIAETGGQNGMIVDSSALAEQVVFDVIASAFDSAGQRCSA 843

Query: 846  LRILCLQEDVADRTLAMLKGAMRELRIGNPDRLAVDVGPVISEEARATIAAHIEAMRAKG 905
            LR+LCLQEDVADRTL MLKGA++EL IG  D+L++D+GPVI+  A+  I +HIE MR+ G
Sbjct: 844  LRVLCLQEDVADRTLTMLKGALKELTIGRTDKLSIDIGPVINTGAKEEIESHIERMRSLG 903

Query: 906  RNVEFLPLPAETADGTFIAPTVIEIGGIHELEREVFGPVLHVVRFHRDDLDALVDSINAT 965
              VE LPLP     GTF+APT+IE+  + +L REVFGPVLHV+R+ R+DLD L+D +N +
Sbjct: 904  CKVEQLPLPRAAELGTFVAPTIIELKKMSDLTREVFGPVLHVMRYRREDLDRLIDEVNNS 963

Query: 966  GYGLTFGLHTRIDATIERVTGRIGAGNVYVNRNTIGAVVGVQPFGGHGLSGTGPKAGGPL 1025
            GYGLTFGLHTR+D TIE VT RI AGN+YVNRN IGAVVGVQPFGG GLSGTGPKAGGPL
Sbjct: 964  GYGLTFGLHTRLDETIEHVTSRIKAGNLYVNRNIIGAVVGVQPFGGRGLSGTGPKAGGPL 1023

Query: 1026 YLSRLLSRRPKGWLEFRGPDAARAAGLAYGEWLRAKGFTAEASRCAGYVARSAIGGGAEL 1085
            Y+ RL+ R P       G      A   +  WL  +G  A+A         SA+G   EL
Sbjct: 1024 YIGRLVQRAPVP--PRHGSVHTDPALREFASWLGRRGHNADADAARDLADVSALGLDQEL 1081

Query: 1086 NGPVGERNLYELHGRGRVLLLPQTRTGLLLQLGAVLATGNSAAVDAPPDLAELLRGLPPA 1145
             GPVGERNLY LH RGR+LL+P+T+ GL  QL A LATGN   +D   +L   L  +P +
Sbjct: 1082 AGPVGERNLYALHPRGRILLVPKTQRGLFRQLAAALATGNEVVIDKASNLENALNSVPAS 1141

Query: 1146 LAARVRTTADWRDVGPLAAVLVEGDRERVTAINRRVADLPGPILLVQAATAEALAAGRGE 1205
            +AAR+  +ADW   GP A  LVEGD  RV  +N+R+A L GP++LVQAAT E LA   G 
Sbjct: 1142 IAARLSWSADWNSAGPFAGALVEGDVSRVQEVNKRIAALDGPLVLVQAATPEELAKDAG- 1200

Query: 1206 GYDLDLLLNERSVSVNTAAAGGNASLVAM 1234
             Y L+ LL E S S+NTAAAGGNA+L+ +
Sbjct: 1201 AYCLNWLLEEVSTSINTAAAGGNANLMTI 1229


Lambda     K      H
   0.319    0.136    0.396 

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: 3633
Number of extensions: 147
Number of successful extensions: 6
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: 1235
Length of database: 1230
Length adjustment: 47
Effective length of query: 1188
Effective length of database: 1183
Effective search space:  1405404
Effective search space used:  1405404
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 59 (27.3 bits)

Align candidate YP_002826548.1 NGR_c20320 (bifunctional proline dehydrogenase/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.43670.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   7.5e-216  703.3   0.5   7.5e-216  703.3   0.5    1.5  2  NCBI__GCF_000018545.1:YP_002826548.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000018545.1:YP_002826548.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  703.3   0.5  7.5e-216  7.5e-216       1     497 [.     536    1030 ..     536    1033 .. 0.98
   2 ?   -3.4   0.1      0.14      0.14     180     196 ..    1112    1128 ..    1110    1131 .. 0.82

  Alignments for each domain:
  == domain 1  score: 703.3 bits;  conditional E-value: 7.5e-216
                             TIGR01238    1 dlygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqvsea 71  
                                            dlyg+ r ns+G+dl+ne++l++l ++l+++++++++a p++  +   eg+++pv+npad++d+vG v+e 
  NCBI__GCF_000018545.1:YP_002826548.1  536 DLYGRERANSKGLDLSNEDTLADLASRLQATVTQDWHATPLL-ADGSLEGKTRPVVNPADHNDVVGSVTEL 605 
                                            89****************************************.667789********************** PP

                             TIGR01238   72 daaevqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevreavdfl 142 
                                              +++++    a + +a+w at ++era +ler+adl+++++  l+a+++reaGk+  na+ evrea+dfl
  NCBI__GCF_000018545.1:YP_002826548.1  606 AVEDASRIARMAAEGAAQWAATSPAERADCLERAADLMQERLEVLMAIAMREAGKSAANAVGEVREAIDFL 676 
                                            *********************************************************************** PP

                             TIGR01238  143 ryyakqvedvldeesakalGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsliaaravellqea 213 
                                            ryya q++++l+   + +lGav+cispwnfplaiftGq+aaal+aGn+v+akpa  t++ia ++v++l+ea
  NCBI__GCF_000018545.1:YP_002826548.1  677 RYYAVQARKTLGPS-HAPLGAVLCISPWNFPLAIFTGQVAAALVAGNSVMAKPAGVTPIIAFESVKILHEA 746 
                                            ***********987.9******************************************************* PP

                             TIGR01238  214 GvpagviqllpGrGedvGaaltsderiaGviftGstevarlinkalakredap...vpliaetGGqnamiv 281 
                                            Gvp g++q++pG G  +Gaal + +  aGv+ftGstevar+i+ +la+r  a    +pliaetGGqn miv
  NCBI__GCF_000018545.1:YP_002826548.1  747 GVPRGALQFIPGSGR-LGAALVAAPETAGVMFTGSTEVARQIQAQLAERLSASgkpIPLIAETGGQNGMIV 816 
                                            **************9.*********************************9886666*************** PP

                             TIGR01238  282 dstalaeqvvadvlasafdsaGqrcsalrvlcvqedvadrvltlikGamdelkvgkpirlttdvGpvidae 352 
                                            ds+alaeqvv dv+asafdsaGqrcsalrvlc+qedvadr+lt++kGa++el +g+  +l  d+Gpvi+  
  NCBI__GCF_000018545.1:YP_002826548.1  817 DSSALAEQVVFDVIASAFDSAGQRCSALRVLCLQEDVADRTLTMLKGALKELTIGRTDKLSIDIGPVINTG 887 
                                            *********************************************************************** PP

                             TIGR01238  353 akqnllahiekmkakakkvaqvkleddvesekgtfvaptlfelddldelkkevfGpvlhvvrykadeldkv 423 
                                            ak+++++hie+m++ + kv q+ l    ++e gtfvapt++el+++++l +evfGpvlhv+ry++++ld++
  NCBI__GCF_000018545.1:YP_002826548.1  888 AKEEIESHIERMRSLGCKVEQLPLPR--AAELGTFVAPTIIELKKMSDLTREVFGPVLHVMRYRREDLDRL 956 
                                            **********************9987..999**************************************** PP

                             TIGR01238  424 vdkinakGygltlGvhsrieetvrqiekrakvGnvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplylyr 494 
                                            +d++n++Gyglt+G+h+r +et+ ++++r+k+Gn+yvnrn++GavvGvqpfGG+GlsGtGpkaGGply+ r
  NCBI__GCF_000018545.1:YP_002826548.1  957 IDEVNNSGYGLTFGLHTRLDETIEHVTSRIKAGNLYVNRNIIGAVVGVQPFGGRGLSGTGPKAGGPLYIGR 1027
                                            *********************************************************************** PP

                             TIGR01238  495 ltr 497 
                                            l++
  NCBI__GCF_000018545.1:YP_002826548.1 1028 LVQ 1030
                                            997 PP

  == domain 2  score: -3.4 bits;  conditional E-value: 0.14
                             TIGR01238  180 qiaaalaaGntviakpa 196 
                                            q+aaala+Gn v+   a
  NCBI__GCF_000018545.1:YP_002826548.1 1112 QLAAALATGNEVVIDKA 1128
                                            899*******9986554 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (500 nodes)
Target sequences:                          1  (1230 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 30.95
//
[ok]

This GapMind analysis is from Sep 24 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