Alignments for a candidate for putA in Cereibacter sphaeroides ATCC 17029

GapMind for catabolism of small carbon sources

Alignments for a candidate for putA in Cereibacter sphaeroides ATCC 17029

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88); Proline dehydrogenase (EC 1.5.5.2) (characterized)
to candidate WP_011840638.1 RSPH17029_RS04265 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA

Query= reanno::Phaeo:GFF1160
         (1158 letters)



>NCBI__GCF_000015985.1:WP_011840638.1
          Length = 1146

 Score = 1408 bits (3645), Expect = 0.0
 Identities = 759/1138 (66%), Positives = 876/1138 (76%), Gaps = 29/1138 (2%)

Query: 34   VDQAQMRDQLFALANLDATDRSTISANAAALVRDIRGHSSPGLMEVFLAEYGLSTDEGVA 93
            +D+A +  +L A A+LD + R+ I A  A LVR IR  S PGLME FLAEYGLSTDEG+A
Sbjct: 14   LDEAGLVARLIAEADLDPSARARIVARGADLVRRIRQGSRPGLMEGFLAEYGLSTDEGIA 73

Query: 94   LMCLAEALLRVPDADTIDALIEDKIAPSEWGKHLGKSTSSLVNASTWALMLTGKVLDEKR 153
            LMCLAEALLRVPDA+T+DALIEDKIAPS+W +HLG+S SSLVNASTWALMLTGKVLD++ 
Sbjct: 74   LMCLAEALLRVPDAETMDALIEDKIAPSDWNRHLGRSASSLVNASTWALMLTGKVLDDRE 133

Query: 154  SPVSA-LRGAMKRLGEPVIRTAVSRAMKEMGRQFVLGETIEGAMKRAAGMEAKGYTYSYD 212
              V+  LRG ++RLGEPVIR AV+RAMKEMGRQFVLGETIEGAM+RAA +EAKGY+YSYD
Sbjct: 134  PGVAGHLRGLVRRLGEPVIRKAVARAMKEMGRQFVLGETIEGAMERAAELEAKGYSYSYD 193

Query: 213  MLGEAARTEADAARYHLAYSRAISAIAAACNSADIRQNPGISVKLSALHPRYELAQETSV 272
            MLGEAARTEADA RYHLAYSRAI+AIAAA  S DIR NPGISVKLSALHPRYE+A+   V
Sbjct: 194  MLGEAARTEADARRYHLAYSRAITAIAAAAKSRDIRDNPGISVKLSALHPRYEVAKRARV 253

Query: 273  KEQLVPRLQALALLAKAAGMGLNVDAEEADRLSLSLEVIEEVISDPALAGWDGFGVVVQA 332
              +LVPR+ ALA LA+AAG+G N+DAEEADRL LSLEVI   +++P+LAGWDGFGVVVQA
Sbjct: 254  LAELVPRVTALAGLARAAGLGFNIDAEEADRLDLSLEVIAAALAEPSLAGWDGFGVVVQA 313

Query: 333  YGPRTGAALDALYDMANRYDRRLMVRLVKGAYWDTEVKRAQVEGVDGFPVFTHKSLTDVS 392
            YG R G  LD LY MA R DR+LMVRLVKGAYWD EVKRAQV G+  FPVFT K  TDVS
Sbjct: 314  YGRRAGEVLDRLYGMAVRLDRKLMVRLVKGAYWDGEVKRAQVLGLADFPVFTRKMATDVS 373

Query: 393  YIANARKLLSITDRIYPQFATHNAHTVSAILHMAKDTDKGAYEFQRLHGMGETLHNMVLE 452
            YIA ARKL S++DRIYPQFATHNAHTV+AIL +A+      +EFQRLHGMGE LH++VL 
Sbjct: 374  YIAQARKLFSMSDRIYPQFATHNAHTVAAILELAEGR---PFEFQRLHGMGERLHDLVLT 430

Query: 453  QNQTHCRIYAPVGAHRDLLAYLVRRLLENGANSSFVNQIVDENVPPELVAADPFAQVEDL 512
            + +T CRIYAPVGAHRDLLAYLVRRLLENGANSSFVNQIVDE+V PE VAA P   +E  
Sbjct: 431  EEKTRCRIYAPVGAHRDLLAYLVRRLLENGANSSFVNQIVDESVSPEAVAACPLTAMERT 490

Query: 513  ----TANLRKGPDLFQPERPNSIGFDLGHAPTLAAIDAARAPWKSHSWAAEPLLAKAPET 568
                   LR G DLF P R NS GFDL  A  LA I++AR+P ++  + A P+LA++   
Sbjct: 491  EPVRNPVLRAGTDLF-PGRRNSRGFDLAAAEDLALIESARSPHRTALFDARPILAES--L 547

Query: 569  ATTTDEPVRNPADLTTVGRVQTAGQAEIETALSAATPWNASAETRAEVLNRAADLYEANY 628
            A      V +PA    VG V  A   ++ETAL  A PW A  E RAEVL RAADLYEA++
Sbjct: 548  AGGQRAEVTDPATGARVGNVLPASLPDVETALHHAVPWEARPEDRAEVLRRAADLYEASF 607

Query: 629  GELFALLTREAGKTLPDCVAELREAVDFLRYYAARISA--EPPVGVFTCISPWNFPLAIF 686
            G +FALL REAGKTLPD V ELREAVDFLRYYAA   A   PP+G   CISPWNFPLAIF
Sbjct: 608  GPIFALLAREAGKTLPDAVGELREAVDFLRYYAAEGEALTAPPLGTVVCISPWNFPLAIF 667

Query: 687  SGQIAAALAVGNAVLAKPAEQTPLIAHRAISLLHEAGVPRSALQLLPG-AGAVGGALTSD 745
            +GQIAAAL  GNAVLAKPAEQTPLIA  A+ LLH AGVP +ALQLLPG  G VG ALT D
Sbjct: 668  TGQIAAALMAGNAVLAKPAEQTPLIAALAVELLHRAGVPATALQLLPGEGGTVGAALTRD 727

Query: 746  ARVGGVAFTGSTATALKIRAAMAEHLRPGAPLIAETGGLNAMIVDSTALPEQAVQSIIES 805
             RVGGV FTGST TA  IR +MA+HL P APLIAETGGLNAMIVDSTALPEQAV+ I+ S
Sbjct: 728  PRVGGVVFTGSTETARAIRQSMADHLDPAAPLIAETGGLNAMIVDSTALPEQAVRDILAS 787

Query: 806  AFQSAGQRCSALRCLYLQEDIADNVLKMLKGAMDALHLGDPWNLSTDSGPVIDETARAGI 865
            AFQSAGQRCSALRCLYLQED+A++VL+ML GAMD L  G+PW+L+TD GPVID  A+AGI
Sbjct: 788  AFQSAGQRCSALRCLYLQEDVAESVLEMLCGAMDELQAGEPWDLATDLGPVIDAEAQAGI 847

Query: 866  LAHIDAARAEGRVLKEMTAPQGGTFVAPTLIEITGIQALEQEIFGPVLHVVRFKSQDLDQ 925
               I AARAEGRVLK+M  P  GTFV PT+I +  I+ +++EIFGPVLHV  F++ ++D+
Sbjct: 848  RDWIAAARAEGRVLKQMAVPARGTFVGPTVIRVGSIREMDREIFGPVLHVATFRATEIDR 907

Query: 926  IIRDINATGYGLTFGLHTRIDDRVQYICDRIHAGNLYVNRNQIGAIVGSQPFGGEGLSGT 985
            +I +I+ATGYGLTFGLH+RIDDRVQ +  R+  GN+YVNRNQIGA+VGSQPFGGEGLSGT
Sbjct: 908  VIAEIDATGYGLTFGLHSRIDDRVQALVGRLRVGNIYVNRNQIGAVVGSQPFGGEGLSGT 967

Query: 986  GPKAGGPFYMMRFCAPDRQKSVDSWPSDAP---------AMTMLPAPTGQPMQEITTSLP 1036
            GPKAGGP Y+ R  +   + + D   S+AP         A+  L    G+ +   T +LP
Sbjct: 968  GPKAGGPAYLARLVS---RPAPDCAGSEAPAQPAAEVQAALDRLAPKAGELIG--TRALP 1022

Query: 1037 GPTGESNRLSQLARPPLLCLGPGPQAVVAQARAVHALGGTAIEATGPLDMRQLLTMEGTS 1096
            GPTGESNRLS L RPPLLCLGPGP A  AQA AV ALGG A+EA G L    L T+ G +
Sbjct: 1023 GPTGESNRLSLLRRPPLLCLGPGPAAARAQAEAVQALGGLAVEAPG-LAPEALATLRGFA 1081

Query: 1097 GVIWWGDETTAREIESWLARRNGPILPLIPGLPDKARVQAERHVCVDTTAAGGNAALL 1154
            G ++WG    AR     LA R G ILPLI GLPD+A V  ERH+C+DTTA+GGNA LL
Sbjct: 1082 GALYWGGAGDARPRAQALASREGAILPLIGGLPDEAHVAVERHLCIDTTASGGNAELL 1139


Lambda     K      H
   0.317    0.132    0.387 

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: 3159
Number of extensions: 147
Number of successful extensions: 11
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: 1158
Length of database: 1146
Length adjustment: 47
Effective length of query: 1111
Effective length of database: 1099
Effective search space:  1220989
Effective search space used:  1220989
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: 58 (26.9 bits)

Align candidate WP_011840638.1 RSPH17029_RS04265 (bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA)
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.452784.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.8e-188  611.4   0.1   1.1e-187  610.5   0.1    1.4  1  NCBI__GCF_000015985.1:WP_011840638.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000015985.1:WP_011840638.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  610.5   0.1  1.1e-187  1.1e-187       3     497 ..     505     982 ..     503     985 .. 0.96

  Alignments for each domain:
  == domain 1  score: 610.5 bits;  conditional E-value: 1.1e-187
                             TIGR01238   3 ygegrknslGvdlaneselksleeqllkaaakkfqaapivgekakaegeaqpvknpadrkdivGqvseadaae 75 
                                           +  gr+ns G dla  + l+ +e+      +  f+a pi++e + a g+   v++pa     vG+v  a++ +
  NCBI__GCF_000015985.1:WP_011840638.1 505 FP-GRRNSRGFDLAAAEDLALIESARSPHRTALFDARPILAE-SLAGGQRAEVTDPATG-ARVGNVLPASLPD 574
                                           54.5************************************55.567888888****975.68*********** PP

                             TIGR01238  76 vqeavdsavaafaewsatdakeraailerladlleshmpelvallvreaGktlsnaiaevreavdflryyakq 148
                                           v+ a++ av     w+a + ++ra +l+r+adl e     + all reaGktl +a+ e+reavdflryya +
  NCBI__GCF_000015985.1:WP_011840638.1 575 VETALHHAV----PWEARP-EDRAEVLRRAADLYEASFGPIFALLAREAGKTLPDAVGELREAVDFLRYYAAE 642
                                           999988776....699975.79*************************************************** PP

                             TIGR01238 149 vedvldeesakalGavvcispwnfplaiftGqiaaalaaGntviakpaeqtsliaaravellqeaGvpagviq 221
                                             +     +a +lG+vvcispwnfplaiftGqiaaal+aGn+v+akpaeqt+liaa avell+ aGvpa+++q
  NCBI__GCF_000015985.1:WP_011840638.1 643 G-EA---LTAPPLGTVVCISPWNFPLAIFTGQIAAALMAGNAVLAKPAEQTPLIAALAVELLHRAGVPATALQ 711
                                           9.44...46779************************************************************* PP

                             TIGR01238 222 llpGrGedvGaaltsderiaGviftGstevarlinkalakredapvpliaetGGqnamivdstalaeqvvadv 294
                                           llpG G +vGaalt d+r++Gv+ftGste+ar i++++a+  d+ +pliaetGG namivdstal+eq v+d+
  NCBI__GCF_000015985.1:WP_011840638.1 712 LLPGEGGTVGAALTRDPRVGGVVFTGSTETARAIRQSMADHLDPAAPLIAETGGLNAMIVDSTALPEQAVRDI 784
                                           ************************************************************************* PP

                             TIGR01238 295 lasafdsaGqrcsalrvlcvqedvadrvltlikGamdelkvgkpirlttdvGpvidaeakqnllahiekmkak 367
                                           lasaf+saGqrcsalr l++qedva+ vl+++ Gamdel+ g+p  l td+Gpvidaea+  +   i + +a 
  NCBI__GCF_000015985.1:WP_011840638.1 785 LASAFQSAGQRCSALRCLYLQEDVAESVLEMLCGAMDELQAGEPWDLATDLGPVIDAEAQAGIRDWIAAARAE 857
                                           ************************************************************************* PP

                             TIGR01238 368 akkvaqvkleddvesekgtfvaptlfelddldelkkevfGpvlhvvrykadeldkvvdkinakGygltlGvhs 440
                                           ++ ++q+   +     +gtfv pt++ + ++ e+++e+fGpvlhv  ++a e+d+v+ +i+a+Gyglt+G+hs
  NCBI__GCF_000015985.1:WP_011840638.1 858 GRVLKQMAVPA-----RGTFVGPTVIRVGSIREMDREIFGPVLHVATFRATEIDRVIAEIDATGYGLTFGLHS 925
                                           *******9998.....9******************************************************** PP

                             TIGR01238 441 rieetvrqiekrakvGnvyvnrnlvGavvGvqpfGGeGlsGtGpkaGGplylyrltr 497
                                           ri++ v+ + +r +vGn+yvnrn++GavvG qpfGGeGlsGtGpkaGGp yl rl++
  NCBI__GCF_000015985.1:WP_011840638.1 926 RIDDRVQALVGRLRVGNIYVNRNQIGAVVGSQPFGGEGLSGTGPKAGGPAYLARLVS 982
                                           ******************************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (500 nodes)
Target sequences:                          1  (1146 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 30.81
//
[ok]

This GapMind analysis is from Apr 10 2024. 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