Alignments for a candidate for fadA in Moritella dasanensis ArB 0140

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Moritella dasanensis ArB 0140

Align Acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate WP_017223438.1 A923_RS0119825 acetyl-CoA C-acyltransferase FadA

Query= reanno::ANA3:7022768
         (387 letters)



>NCBI__GCF_000276805.1:WP_017223438.1
          Length = 389

 Score =  606 bits (1562), Expect = e-178
 Identities = 305/387 (78%), Positives = 336/387 (86%)

Query: 1   MKQAVIVDCIRTPMGRSKAGVFRNVRAETLSAELMKGLLLRNPQLDPNTIEDVIWGCVQQ 60
           M+  V+VDC+RTPMGRSKAG FR+VRAE LSA+LM+GLL RNP++DPN IEDV WGCVQQ
Sbjct: 1   MRDVVVVDCLRTPMGRSKAGAFRHVRAEDLSAKLMRGLLDRNPEVDPNDIEDVYWGCVQQ 60

Query: 61  TLEQGFNIARNASLLAGIPKTAGAVTVNRLCGSSMEAIHQAARAIMTGMGDTFIIGGVEH 120
           TLEQGFNIARNASLLAGIP TAGA TVNRLCGSSM+AIH A RAI  G GD  IIGGVEH
Sbjct: 61  TLEQGFNIARNASLLAGIPITAGATTVNRLCGSSMQAIHDATRAIAMGDGDVMIIGGVEH 120

Query: 121 MGHVPMNHGVDFHPGLANNVAKASGMMGLTAEMLGKLHGITREQQDAFAVRSHQRAHAAT 180
           MGHVPMNHGVDFH GLA + AKA+GMMGLTAEMLGK+HGITREQQDAFAVRSH+ A AAT
Sbjct: 121 MGHVPMNHGVDFHVGLAKSTAKAAGMMGLTAEMLGKMHGITREQQDAFAVRSHKLAQAAT 180

Query: 181 VEGRFAKEIYGIEGHDANGALIKVLHDEVIRPETSMESLAALRPVFDPANGTVTAGTSSA 240
           V GRF +EI  IEGHDA+G L     DEVIRPET+MESLA LRPVFDP NGTVTAGTSSA
Sbjct: 181 VSGRFKREILPIEGHDADGILKLYDFDEVIRPETTMESLAGLRPVFDPVNGTVTAGTSSA 240

Query: 241 LSDGASAMLVMEESKARALGLPIRARIRSMAVAGCDAAIMGYGPVPATQKALARAGITVN 300
           LSDGASAML+M   KA+ LGL  RAR+ SMAVAGCD +IMGYGPVPAT+KAL RAG+T+N
Sbjct: 241 LSDGASAMLLMSADKAKELGLKPRARVVSMAVAGCDPSIMGYGPVPATKKALKRAGLTIN 300

Query: 301 DLDVIELNEAFAAQSLPCVKDLGLLDVVEDKINLNGGAIALGHPLGCSGARISTTLINLM 360
           D+DV ELNEAFAAQSLPCVKDLGL DVVE KINLNGGAI+LGHPLGCSG+RISTTL+N +
Sbjct: 301 DIDVFELNEAFAAQSLPCVKDLGLEDVVETKINLNGGAISLGHPLGCSGSRISTTLVNEL 360

Query: 361 EHKDATLGLATMCIGLGQGIATVFERV 387
           E +    GLATMCIGLGQGIAT+FER+
Sbjct: 361 EVQGGRYGLATMCIGLGQGIATIFERI 387


Lambda     K      H
   0.320    0.134    0.386 

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: 585
Number of extensions: 14
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: 387
Length of database: 389
Length adjustment: 30
Effective length of query: 357
Effective length of database: 359
Effective search space:   128163
Effective search space used:   128163
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: 50 (23.9 bits)

Align candidate WP_017223438.1 A923_RS0119825 (acetyl-CoA C-acyltransferase FadA)
to HMM TIGR02445 (fadA: acetyl-CoA C-acyltransferase FadA (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/TIGR02445.hmm
# target sequence database:        /tmp/gapView.3640611.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR02445  [M=385]
Accession:   TIGR02445
Description: fadA: acetyl-CoA C-acyltransferase FadA
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   6.4e-224  728.9   5.9   7.2e-224  728.7   5.9    1.0  1  NCBI__GCF_000276805.1:WP_017223438.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000276805.1:WP_017223438.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  728.7   5.9  7.2e-224  7.2e-224       1     385 []       3     387 ..       3     387 .. 1.00

  Alignments for each domain:
  == domain 1  score: 728.7 bits;  conditional E-value: 7.2e-224
                             TIGR02445   1 dvvivdalrtpmgrskggafrntraedlsahllkkllarnpkveaaevediywgcvqqtleqgfniarnaall 73 
                                           dvv+vd+lrtpmgrsk gafr++raedlsa+l+++ll+rnp+v++ ++ed+ywgcvqqtleqgfniarna+ll
  NCBI__GCF_000276805.1:WP_017223438.1   3 DVVVVDCLRTPMGRSKAGAFRHVRAEDLSAKLMRGLLDRNPEVDPNDIEDVYWGCVQQTLEQGFNIARNASLL 75 
                                           79*********************************************************************** PP

                             TIGR02445  74 aevphevaavtvnrlcgssmqalhdaaraimtgdaevcliggvehmghvsmshgvdfhpglskhvakaagmmg 146
                                           a++p++ +a tvnrlcgssmqa+hda+rai  gd++v++iggvehmghv+m+hgvdfh gl+k +akaagmmg
  NCBI__GCF_000276805.1:WP_017223438.1  76 AGIPITAGATTVNRLCGSSMQAIHDATRAIAMGDGDVMIIGGVEHMGHVPMNHGVDFHVGLAKSTAKAAGMMG 148
                                           ************************************************************************* PP

                             TIGR02445 147 ltaemlgklhgisreqqdafaarsharahaatlegkfkneiiptegydadgvlkvldydevirpettvealaa 219
                                           ltaemlgk+hgi+reqqdafa+rsh++a aat++g+fk ei+p+eg+dadg+lk +d+devirpett+e+la 
  NCBI__GCF_000276805.1:WP_017223438.1 149 LTAEMLGKMHGITREQQDAFAVRSHKLAQAATVSGRFKREILPIEGHDADGILKLYDFDEVIRPETTMESLAG 221
                                           ************************************************************************* PP

                             TIGR02445 220 lrpafdpkngtvtagtssalsdgasamlvmseeraqelgvkprarirsmavagvdpsimgygpvpatkkalkr 292
                                           lrp+fdp+ngtvtagtssalsdgasaml+ms+++a+elg+kprar+ smavag+dpsimgygpvpatkkalkr
  NCBI__GCF_000276805.1:WP_017223438.1 222 LRPVFDPVNGTVTAGTSSALSDGASAMLLMSADKAKELGLKPRARVVSMAVAGCDPSIMGYGPVPATKKALKR 294
                                           ************************************************************************* PP

                             TIGR02445 293 aglsisdidvlelneafaaqalpvlkdlglldkldekvnlnggaialghplgcsgaristtllnlmerkdakf 365
                                           agl+i+didv+elneafaaq+lp++kdlgl d+++ k+nlnggai+lghplgcsg+risttl+n +e +++++
  NCBI__GCF_000276805.1:WP_017223438.1 295 AGLTINDIDVFELNEAFAAQSLPCVKDLGLEDVVETKINLNGGAISLGHPLGCSGSRISTTLVNELEVQGGRY 367
                                           ************************************************************************* PP

                             TIGR02445 366 glatmciglgqgiatvferv 385
                                           glatmciglgqgiat+fer+
  NCBI__GCF_000276805.1:WP_017223438.1 368 GLATMCIGLGQGIATIFERI 387
                                           ******************95 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (389 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 22.87
//
[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