Alignments for a candidate for fadA in Rhizobium leguminosarum WSM1325

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Rhizobium leguminosarum WSM1325

Align acetyl-CoA:acetyl-CoA C-acetyltransferase / acetyl-CoA:propanoyl-CoA 2-C-acetyltransferase (EC 2.3.1.9; EC 2.3.1.16) (characterized)
to candidate WP_012760742.1 RLEG_RS35140 acetyl-CoA C-acyltransferase

Query= reanno::pseudo3_N2E3:AO353_25685
         (397 letters)



>NCBI__GCF_000023185.1:WP_012760742.1
          Length = 395

 Score =  555 bits (1430), Expect = e-163
 Identities = 276/389 (70%), Positives = 329/389 (84%)

Query: 6   DPIVIVSAVRTPMGGFQGELKSLSAPQLGAAAIRAAVERAGVAADAVEEVLFGCVLSAGL 65
           DPIVIV A RTP+G FQGELK  +AP+LGA AIRAA++R+ V A+A+EEV+FGCVL AG 
Sbjct: 5   DPIVIVGAARTPIGSFQGELKEATAPELGATAIRAALQRSRVEAEAIEEVVFGCVLPAGQ 64

Query: 66  GQAPARQAALGAGLDKSTRCTTLNKMCGSGMEAAILAHDMLLAGSADVVVAGGMESMSNA 125
           GQAPARQAA+ AGL  +T  +T+NKMCGSGM+A ++AHD++ AGSA V VAGGMESM+NA
Sbjct: 65  GQAPARQAAIHAGLPFATAASTVNKMCGSGMKAVMIAHDLIAAGSASVAVAGGMESMTNA 124

Query: 126 PYLLDRARSGYRMGHGKVLDHMFLDGLEDAYDKGRLMGTFAEDCAEANGFTREAQDEFAI 185
           PYLLD+AR GYR+GHG+V+DHMFLDGLEDAYDKGRLMG+FAEDCAEA  FTREAQD +AI
Sbjct: 125 PYLLDKARGGYRLGHGRVVDHMFLDGLEDAYDKGRLMGSFAEDCAEAYQFTREAQDSYAI 184

Query: 186 ASTTRAQQAIKDGSFNAEIVPLQVIVGKEQKLITDDEQPPKAKLDKIASLKPAFRDGGTV 245
           AS TRAQ+AI +G F +EI P+ V  GK +++ + DEQP KAKLDKI +LKPAFR+GGTV
Sbjct: 185 ASLTRAQKAIAEGCFESEIAPVTVKSGKAEQVASRDEQPDKAKLDKIPTLKPAFREGGTV 244

Query: 246 TAANSSSISDGAAALLLMRRSEAEKRGLKPLAVIHGHAAFADTPGLFPVAPVGAIKKLLK 305
           TAANSSSISDGAAAL+LMRRSEAE+RGLKPLA I GHA  +  P LF  AP+GA++KL  
Sbjct: 245 TAANSSSISDGAAALVLMRRSEAERRGLKPLATILGHATHSQAPNLFATAPIGALQKLSD 304

Query: 306 KTGWSLDEVELFEVNEAFAVVSLVTMTKLEIPHSKVNVHGGACALGHPIGASGARILVTL 365
           +TG  L  V+LFE+NEAFAVV++  M  L +PH KVNVHGGACALGHPIGASGARILVTL
Sbjct: 305 RTGLPLSAVDLFEINEAFAVVAMAAMRDLNLPHEKVNVHGGACALGHPIGASGARILVTL 364

Query: 366 LSALRQKGLKRGVAAICIGGGEATAMAVE 394
           L+AL +  LKRG+AA+CIGGGEATA+A+E
Sbjct: 365 LAALERYDLKRGMAALCIGGGEATAVAIE 393


Lambda     K      H
   0.318    0.133    0.378 

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: 522
Number of extensions: 9
Number of successful extensions: 1
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: 397
Length of database: 395
Length adjustment: 31
Effective length of query: 366
Effective length of database: 364
Effective search space:   133224
Effective search space used:   133224
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: 50 (23.9 bits)

Align candidate WP_012760742.1 RLEG_RS35140 (acetyl-CoA C-acyltransferase)
to HMM TIGR01930 (acetyl-CoA C-acyltransferase (EC 2.3.1.16))

# 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/TIGR01930.hmm
# target sequence database:        /tmp/gapView.7325.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01930  [M=385]
Accession:   TIGR01930
Description: AcCoA-C-Actrans: acetyl-CoA C-acyltransferase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   8.2e-131  422.4   9.0   9.3e-131  422.2   9.0    1.0  1  lcl|NCBI__GCF_000023185.1:WP_012760742.1  RLEG_RS35140 acetyl-CoA C-acyltr


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000023185.1:WP_012760742.1  RLEG_RS35140 acetyl-CoA C-acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  422.2   9.0  9.3e-131  9.3e-131       1     385 []       9     393 ..       9     393 .. 0.97

  Alignments for each domain:
  == domain 1  score: 422.2 bits;  conditional E-value: 9.3e-131
                                 TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaag 69 
                                               iv+a+Rtpig+++g lke++a +L+a++i+++l+r+ +++e+i+ev++G+vl+ag+++++aR+aa+ ag
  lcl|NCBI__GCF_000023185.1:WP_012760742.1   9 IVGAARTPIGSFQGELKEATAPELGATAIRAALQRSRVEAEAIEEVVFGCVLPAGQGQAPARQAAIHAG 77 
                                               89******************************************************************* PP

                                 TIGR01930  70 lpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakled 138
                                               lp  ++a tvn++C+Sg++Av++a + i+aG a+v+vaGG+Esm+++p+ll+++  r +++lg+ ++ d
  lcl|NCBI__GCF_000023185.1:WP_012760742.1  78 LPFATAASTVNKMCGSGMKAVMIAHDLIAAGSASVAVAGGMESMTNAPYLLDKA--RGGYRLGHGRVVD 144
                                               ****************************************************98..89*********** PP

                                 TIGR01930 139 qllkdl....vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk.. 201
                                               ++  d+     +++  mg  Ae +a+ y+++Re qD+ya++S ++a+kAi+eg f++ei pv+vk    
  lcl|NCBI__GCF_000023185.1:WP_012760742.1 145 HMFLDGledaYDKGRLMGSFAEDCAEAYQFTREAQDSYAIASLTRAQKAIAEGCFESEIAPVTVKSGka 213
                                               999999999888999*************************************************98896 PP

                                 TIGR01930 202 kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplariv 270
                                               ++v s+De++ ++ +l+k+ +Lkpaf+e  g tvtA+Nss+++DGAaal+lm ++ a++ gl+pla+i 
  lcl|NCBI__GCF_000023185.1:WP_012760742.1 214 EQVASRDEQP-DKAKLDKIPTLKPAFRE-GG-TVTAANSSSISDGAAALVLMRRSEAERRGLKPLATIL 279
                                               6776777766.599************96.68.7************************************ PP

                                 TIGR01930 271 saavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAi 339
                                               ++a+ +  p+ + ++p+ A +k+ +++gl +s +dl+EinEAFA++++a++++l+ l +ekvNv+GGA 
  lcl|NCBI__GCF_000023185.1:WP_012760742.1 280 GHATHSQAPNLFATAPIGALQKLSDRTGLPLSAVDLFEINEAFAVVAMAAMRDLN-LPHEKVNVHGGAC 347
                                               *******************************************************.88*********** PP

                                 TIGR01930 340 AlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                               AlGHP+GasGari++tll +L++ + k+G+a+lC+ggG ++Av +e
  lcl|NCBI__GCF_000023185.1:WP_012760742.1 348 ALGHPIGASGARILVTLLAALERYDLKRGMAALCIGGGEATAVAIE 393
                                               *******************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (395 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: 10.90
//
[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