Alignments for a candidate for rocA in Chryseobacterium angstadtii KM

GapMind for catabolism of small carbon sources

Alignments for a candidate for rocA in Chryseobacterium angstadtii KM

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_048506277.1 ACM46_RS08740 L-glutamate gamma-semialdehyde dehydrogenase

Query= BRENDA::Q4DRT8
         (561 letters)



>NCBI__GCF_001045465.1:WP_048506277.1
          Length = 541

 Score =  491 bits (1263), Expect = e-143
 Identities = 255/543 (46%), Positives = 343/543 (63%), Gaps = 7/543 (1%)

Query: 11  AYAKCPTIVNEPMDTFEAGSVSANGTLEACRRMRESVTDCPIVIGGKEYRTDNVIRRTIP 70
           A ++ P  VNEP++++  GS      +   ++M     + P+ I GKE +TD  ++   P
Sbjct: 4   AISQVPFAVNEPVNSYVPGSPEVKSLIATYKKMWAEKIEIPMFINGKEVKTDEKVQLQSP 63

Query: 71  SDHKKHLATSYNATPELAQKAIDTALQASREWSQTSFRDRAAIFLHAAHLISTKYRHELR 130
            DH       Y  T +    AI+ AL A +EW++  +  RAAIFL AA L++  YR  + 
Sbjct: 64  QDHAHDFGFYYKGTMQHVDDAINAALAAKKEWNELGWEQRAAIFLKAADLLAGPYRDVIN 123

Query: 131 AATMLGQSKSPFQAEIDVIAESCDFLRFSVHYAENLYRDQPLSPSSGAVWNSLDYRPLEG 190
           AATM+GQSK+  QAEID   E  DFLRF+V +   +Y +QP+S S   +WN ++YRPLEG
Sbjct: 124 AATMIGQSKNVHQAEIDSACEFIDFLRFNVEFMTEMYSEQPVSDSG--IWNRVEYRPLEG 181

Query: 191 FVSTIAPFNFAAIAANLVACPALMGNVVLWKPSPHAVLSNYLLYKVFEEAGLPAGVVNFL 250
           F   + PFNF AI+ NL  C A++GNVV+WKPS   V S  ++  V  EAGLPAGV+N +
Sbjct: 182 FCFAVTPFNFTAISGNLPTCMAMLGNVVVWKPSDKQVYSAKVIMDVLIEAGLPAGVINMV 241

Query: 251 PCEPDVMTNFVNSHRDLAGVAFTGSTKVFMSINKQIYARLEEYRNIPRISGETGGKDFHL 310
             +       V +HRD AG+ FTGSTKVF  + K I   +  YR  PRI GETGGKDF +
Sbjct: 242 FTDGKETAEKVLAHRDFAGLHFTGSTKVFQGMWKMIGDNIHNYRTYPRIVGETGGKDFVI 301

Query: 311 VHPSADLKLAAALTVRGAFEFQGQKCSATSRLYAPKSRWEELKNYMLGVHEQLKMGQPDD 370
            HPS++++  A   VRG+FE+QGQKCSA SR Y PKS W ++K  M      +K+G P+D
Sbjct: 302 AHPSSNVEAVATALVRGSFEYQGQKCSAASRAYVPKSLWADVKKVMETQINSIKIGSPED 361

Query: 371 FKSFMCAVIDETAFERNKKYIDIAKSSPSTYSVIAGGGYDKTEGWFVQPTIVESKDSQAQ 430
             +F+ AVID+ +FE+ K YID A +S     V  GG  D ++GWFV PT++E+ +   +
Sbjct: 362 PSNFVNAVIDKNSFEKCKGYIDRANASTEA-KVAIGGTCDDSKGWFVHPTVIETTNPHYE 420

Query: 431 LMHEEIFGPILTVHVYDDSKPGFWSDVCDVVNRSTKYALTGSIFAQDRQAIRDATTKHLR 490
            M EEIFGP+LTV VY+D     W +   +V+ ++ Y+LTGS+FAQDR AI +A  K L 
Sbjct: 421 SMVEEIFGPVLTVFVYEDQD---WKETLKLVDSTSPYSLTGSVFAQDRYAINEA-FKALE 476

Query: 491 YAAGNYYINDKCTGAVVGQQPFGGARASGSNDKPGSPLFLTRWVSARTIKENFDHSTQVS 550
            A+GN+YINDK TGAVVGQQPFGG RASG+NDK GS + L RW S R+IKE F       
Sbjct: 477 NASGNFYINDKPTGAVVGQQPFGGGRASGTNDKAGSKMNLLRWTSVRSIKETFVSPKDYK 536

Query: 551 YPH 553
           YP+
Sbjct: 537 YPY 539


Lambda     K      H
   0.320    0.133    0.402 

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: 852
Number of extensions: 37
Number of successful extensions: 5
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: 561
Length of database: 541
Length adjustment: 36
Effective length of query: 525
Effective length of database: 505
Effective search space:   265125
Effective search space used:   265125
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: 53 (25.0 bits)

Align candidate WP_048506277.1 ACM46_RS08740 (L-glutamate gamma-semialdehyde dehydrogenase)
to HMM TIGR01236 (pruA: 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/TIGR01236.hmm
# target sequence database:        /tmp/gapView.919233.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01236  [M=533]
Accession:   TIGR01236
Description: D1pyr5carbox1: 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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.4e-237  774.7   1.7   2.7e-237  774.5   1.7    1.0  1  NCBI__GCF_001045465.1:WP_048506277.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001045465.1:WP_048506277.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  774.5   1.7  2.7e-237  2.7e-237       2     531 ..      13     539 ..      12     541 .] 0.99

  Alignments for each domain:
  == domain 1  score: 774.5 bits;  conditional E-value: 2.7e-237
                             TIGR01236   2 nePvkefrpgskerdllrkelkelkskvleiPlviggkevvksnelievvaPadhqaklakltnateedvkka 74 
                                           nePv+++ pgs+e + l ++ k++  +++eiP+ i+gke vk++e+++ ++P+dh++  +  ++ t ++v +a
  NCBI__GCF_001045465.1:WP_048506277.1  13 NEPVNSYVPGSPEVKSLIATYKKMWAEKIEIPMFINGKE-VKTDEKVQLQSPQDHAHDFGFYYKGTMQHVDDA 84 
                                           9**************************************.677778*************************** PP

                             TIGR01236  75 veaaldakkeWselpfadraaiflkaadllsgkyreeilaatmlgqsktvyqaeidavaelidffrfnvkyar 147
                                           ++aal+akkeW+el +++raaiflkaadll+g+yr  i+aatm+gqsk+v+qaeid+++e idf+rfnv++ +
  NCBI__GCF_001045465.1:WP_048506277.1  85 INAALAAKKEWNELGWEQRAAIFLKAADLLAGPYRDVINAATMIGQSKNVHQAEIDSACEFIDFLRFNVEFMT 157
                                           ************************************************************************* PP

                             TIGR01236 148 elleqqPsvsapgelnkveyrpleGfvaaisPfnftaiaanlagaPalmGnvvvWkPsktavlsnyllmkile 220
                                           e+++ qP vs +g +n+veyrpleGf +a++Pfnftai++nl+++ a++GnvvvWkPs+ +v+s+ ++m +l 
  NCBI__GCF_001045465.1:WP_048506277.1 158 EMYSEQP-VSDSGIWNRVEYRPLEGFCFAVTPFNFTAISGNLPTCMAMLGNVVVWKPSDKQVYSAKVIMDVLI 229
                                           *******.7**************************************************************** PP

                             TIGR01236 221 eaGlPpgvinfvpadgvkvsdvvladkdlaalhftGstavfkelwkkvasnldkyrnfPrivGetGGkdfvlv 293
                                           eaGlP+gvin+v +dg + +++vla++d+a+lhftGst+vf+ +wk++  n+++yr++PrivGetGGkdfv++
  NCBI__GCF_001045465.1:WP_048506277.1 230 EAGLPAGVINMVFTDGKETAEKVLAHRDFAGLHFTGSTKVFQGMWKMIGDNIHNYRTYPRIVGETGGKDFVIA 302
                                           ************************************************************************* PP

                             TIGR01236 294 hpsadveevvaatirgafeyqGqkcsaasrlyvpkslwkelkeellaelkkvkvgdvddlssfmgavideksf 366
                                           hps++ve v++a++rg+feyqGqkcsaasr+yvpkslw ++k+ + ++ +++k+g ++d s+f+ avid++sf
  NCBI__GCF_001045465.1:WP_048506277.1 303 HPSSNVEAVATALVRGSFEYQGQKCSAASRAYVPKSLWADVKKVMETQINSIKIGSPEDPSNFVNAVIDKNSF 375
                                           ************************************************************************* PP

                             TIGR01236 367 akivkviekakkdpeeleilaGGkyddskGyfvePtvveskdPkeklmkeeifGPvltvyvydddkykeilev 439
                                           +k + +i++a +++ e ++++GG +ddskG+fv+Ptv+e+ +P+ ++m+eeifGPvltv+vy+d+ +ke+l++
  NCBI__GCF_001045465.1:WP_048506277.1 376 EKCKGYIDRANAST-EAKVAIGGTCDDSKGWFVHPTVIETTNPHYESMVEEIFGPVLTVFVYEDQDWKETLKL 447
                                           ************76.9********************************************************* PP

                             TIGR01236 440 vdstskyaltGavfakdreaieeaekklrfaaGnfyindkstGavvgqqpfGGarlsGtndkaGapkillrfv 512
                                           vdsts y+ltG+vfa+dr ai+ea k+l +a+Gnfyindk+tGavvgqqpfGG r+sGtndkaG+  +llr++
  NCBI__GCF_001045465.1:WP_048506277.1 448 VDSTSPYSLTGSVFAQDRYAINEAFKALENASGNFYINDKPTGAVVGQQPFGGGRASGTNDKAGSKMNLLRWT 520
                                           ************************************************************************* PP

                             TIGR01236 513 sarsiketfkeltdfkypy 531
                                           s+rsiketf++++d+kypy
  NCBI__GCF_001045465.1:WP_048506277.1 521 SVRSIKETFVSPKDYKYPY 539
                                           ******************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (533 nodes)
Target sequences:                          1  (541 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 21.83
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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