Alignments for a candidate for fadA in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Halomonas desiderata SP1

Align Acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate WP_086510729.1 BZY95_RS15085 acetyl-CoA C-acyltransferase FadA

Query= reanno::SB2B:6935813
         (387 letters)



>NCBI__GCF_002151265.1:WP_086510729.1
          Length = 392

 Score =  498 bits (1282), Expect = e-145
 Identities = 248/386 (64%), Positives = 304/386 (78%)

Query: 2   KQAVIVDCIRTPMGRSKGGVFRNVRAETLSAELMKALLLRNPGVDPNTIEDVIWGCVQQT 61
           +  V+VD +RT M ++K G FRNVRAE LSA +M+AL  RN  +DP  ++DVIWGCV QT
Sbjct: 6   RDIVVVDGVRTAMAKAKNGAFRNVRAENLSAAVMQALFDRNANLDPAEVDDVIWGCVNQT 65

Query: 62  LEQGFNIARNASLLAGVPKTAGAVTVNRLCGSSMEALHQASRAIMTGMGDTFIIGGVEHM 121
           LEQ  NIARNA+++ G+P+T  A TVNRLCGSSM ALH A+  I  GMGD ++IGGVEHM
Sbjct: 66  LEQSMNIARNAAIMTGIPRTVPAQTVNRLCGSSMTALHIAAANIKAGMGDFYVIGGVEHM 125

Query: 122 GHVPMNHGVDFHPGLAANVAKASGMMGLTAEMLGKLHGISREMQDQFAVRSHQRAHAASI 181
            HVPM HGVD +P  +   AKA+ MMGLTAE+LGK+HG++RE QD+F VRSHQRA AAS 
Sbjct: 126 EHVPMAHGVDVNPAASKYAAKAAMMMGLTAELLGKMHGVTREDQDKFGVRSHQRAAAASD 185

Query: 182 EGRFANEIYAIEGHDANGALIKVDYDEVIRPETTLESLAGLRPVFDPANGTVTAGTSSAL 241
           +G F NEI  +EGHD  G    V  DEVIR + +LE +A L+PVFDP  GTV+AGTSSAL
Sbjct: 186 KGYFDNEIVGVEGHDERGFRQLVKRDEVIRIDASLEEMAKLKPVFDPRGGTVSAGTSSAL 245

Query: 242 SDGAAAMLVMEEEKARALGLTIRARVRSMAVAGCDAAIMGYGPVPATQKALARAGLSIQD 301
           S GA+AM +M  E+ARALGL   ARV S  VAGCDA+IMGYGPVPA++KAL  AGLS QD
Sbjct: 246 SVGASAMAIMSYERARALGLEPIARVLSTGVAGCDASIMGYGPVPASKKALKAAGLSAQD 305

Query: 302 MDVIELNEAFAAQSLPCVKDLGLMDVVEDKVNLNGGAIALGHPLGCSGARISTTLINLME 361
           +  +ELNEAFAAQ++P +KDLG ++ +++KVNLNGGAIALGHPLGCSG+RI TTL+N+M 
Sbjct: 306 IQTVELNEAFAAQAIPVLKDLGFLEAMDEKVNLNGGAIALGHPLGCSGSRICTTLLNVMR 365

Query: 362 HKDATLGLATMCIGLGQGIATVFERV 387
            +D TLGLATMCIG+GQG+ATVFER+
Sbjct: 366 QQDTTLGLATMCIGMGQGVATVFERL 391


Lambda     K      H
   0.319    0.134    0.384 

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: 525
Number of extensions: 21
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: 392
Length adjustment: 30
Effective length of query: 357
Effective length of database: 362
Effective search space:   129234
Effective search space used:   129234
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_086510729.1 BZY95_RS15085 (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.18331.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.8e-188  610.3  11.8   7.6e-188  610.1  11.8    1.0  1  lcl|NCBI__GCF_002151265.1:WP_086510729.1  BZY95_RS15085 acetyl-CoA C-acylt


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086510729.1  BZY95_RS15085 acetyl-CoA C-acyltransferase FadA
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  610.1  11.8  7.6e-188  7.6e-188       1     384 [.       7     390 ..       7     391 .. 1.00

  Alignments for each domain:
  == domain 1  score: 610.1 bits;  conditional E-value: 7.6e-188
                                 TIGR02445   1 dvvivdalrtpmgrskggafrntraedlsahllkkllarnpkveaaevediywgcvqqtleqgfniarn 69 
                                               d+v+vd +rt m ++k gafrn+rae+lsa ++++l++rn+++++aev+d++wgcv+qtleq +niarn
  lcl|NCBI__GCF_002151265.1:WP_086510729.1   7 DIVVVDGVRTAMAKAKNGAFRNVRAENLSAAVMQALFDRNANLDPAEVDDVIWGCVNQTLEQSMNIARN 75 
                                               69******************************************************************* PP

                                 TIGR02445  70 aallaevphevaavtvnrlcgssmqalhdaaraimtgdaevcliggvehmghvsmshgvdfhpglskhv 138
                                               aa+++++p +v+a+tvnrlcgssm+alh aa  i +g ++ ++iggvehm hv+m+hgvd++p  sk +
  lcl|NCBI__GCF_002151265.1:WP_086510729.1  76 AAIMTGIPRTVPAQTVNRLCGSSMTALHIAAANIKAGMGDFYVIGGVEHMEHVPMAHGVDVNPAASKYA 144
                                               ********************************************************************* PP

                                 TIGR02445 139 akaagmmgltaemlgklhgisreqqdafaarsharahaatlegkfkneiiptegydadgvlkvldydev 207
                                               akaa mmgltae+lgk+hg++re qd+f++rsh+ra aa+ +g f nei+ +eg+d+ g+ + ++ dev
  lcl|NCBI__GCF_002151265.1:WP_086510729.1 145 AKAAMMMGLTAELLGKMHGVTREDQDKFGVRSHQRAAAASDKGYFDNEIVGVEGHDERGFRQLVKRDEV 213
                                               ********************************************************************* PP

                                 TIGR02445 208 irpettvealaalrpafdpkngtvtagtssalsdgasamlvmseeraqelgvkprarirsmavagvdps 276
                                               ir ++++e +a+l+p+fdp++gtv+agtssals gasam +ms era+ lg++p ar+ s  vag+d s
  lcl|NCBI__GCF_002151265.1:WP_086510729.1 214 IRIDASLEEMAKLKPVFDPRGGTVSAGTSSALSVGASAMAIMSYERARALGLEPIARVLSTGVAGCDAS 282
                                               ********************************************************************* PP

                                 TIGR02445 277 imgygpvpatkkalkraglsisdidvlelneafaaqalpvlkdlglldkldekvnlnggaialghplgc 345
                                               imgygpvpa+kkalk agls++di+ +elneafaaqa+pvlkdlg+l+ +dekvnlnggaialghplgc
  lcl|NCBI__GCF_002151265.1:WP_086510729.1 283 IMGYGPVPASKKALKAAGLSAQDIQTVELNEAFAAQAIPVLKDLGFLEAMDEKVNLNGGAIALGHPLGC 351
                                               ********************************************************************* PP

                                 TIGR02445 346 sgaristtllnlmerkdakfglatmciglgqgiatvfer 384
                                               sg+ri ttlln+m+++d++ glatmcig+gqg+atvfer
  lcl|NCBI__GCF_002151265.1:WP_086510729.1 352 SGSRICTTLLNVMRQQDTTLGLATMCIGMGQGVATVFER 390
                                               **************************************9 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (392 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: 00:00:00.02
# Mc/sec: 7.19
//
[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