Alignments for a candidate for fadA in Ruegeria conchae TW15

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Ruegeria conchae TW15

Align 3-ketoacyl-CoA thiolase (EC 2.3.1.16) (characterized)
to candidate WP_010440841.1 G7G_RS0109505 acetyl-CoA C-acyltransferase

Query= reanno::pseudo13_GW456_L13:PfGW456L13_2982
         (397 letters)



>NCBI__GCF_000192475.1:WP_010440841.1
          Length = 390

 Score =  464 bits (1194), Expect = e-135
 Identities = 242/387 (62%), Positives = 291/387 (75%), Gaps = 2/387 (0%)

Query: 8   IVIVSAVRTPMGGFQGELKSLTAPQLGAAAIKAAVERAGVASDSVDEVLFGCVLPAGLGQ 67
           +VI  A RTPMGGFQG    +TA  LG AAI+AA++ AG  +D+VDEVL GCVLPAG GQ
Sbjct: 4   VVIAGAARTPMGGFQGMFDGVTAADLGGAAIRAALKGAG--ADTVDEVLMGCVLPAGQGQ 61

Query: 68  APARQAALGAGLDKSTRCTTLNKMCGSGMEAAILAHDMLLAGSADVVVAGGMESMSNAPY 127
           APARQA   AGL +    TTLNKMCGSGM+AA++A D +  G    +VAGGMESM+NAPY
Sbjct: 62  APARQAGFAAGLGEEVPATTLNKMCGSGMKAAMIAFDQIALGHTQTMVAGGMESMTNAPY 121

Query: 128 LLDRARAGYRMGHGRVQDSMFLDGLEDAYDKGRLMGTFAEDCAETNGFSREAQDAFAIAS 187
           LL + R G R+GHG+V D MFLDGLEDAYDKGRLMGTFAEDCAE+  F+REAQD +A+ S
Sbjct: 122 LLPKMRGGARIGHGQVVDHMFLDGLEDAYDKGRLMGTFAEDCAESYQFTREAQDEYALRS 181

Query: 188 TTRAQQAIKDGSFKAEIVPLTVTVGKEQVVISNDEQPPKARLDKIASLKPAFREGGTVTA 247
            + A  A ++ +F  EI  +++   K +VV+  DEQP  AR +KI +LKPAFRE GTVTA
Sbjct: 182 LSNALSAQENNAFDQEITSVSIQTRKGEVVLDADEQPQSARPEKIPTLKPAFREDGTVTA 241

Query: 248 ANSSSISDGAAALVLMRQSQAQKQGLKPLAVIHGHAAFADTPGLFPVAPIGAIKKLMKKT 307
           ANSSSISDGAAALVL    +A+KQ L   A I GHA+ A  PGLF  AP+ A +KL+ + 
Sbjct: 242 ANSSSISDGAAALVLASAEEAEKQNLTVRARILGHASHAQAPGLFTTAPVPAAQKLLDRI 301

Query: 308 GWSLNDVDLVEVNEAFAVVGMAAMTHLEIPHEKLNVHGGACALGHPIGASGARILVTLLS 367
           GW   DVDL EVNEAFAVV MA M  + +  E +NV+GGACALGHPIGASGARI+VTLL+
Sbjct: 302 GWKKEDVDLWEVNEAFAVVPMAFMHEMGLSREIVNVNGGACALGHPIGASGARIMVTLLN 361

Query: 368 ALRQKGLKRGVAAICIGGGEATAMAVE 394
           AL ++ LKRGVAAICIGGGE TA+A+E
Sbjct: 362 ALEKRDLKRGVAAICIGGGEGTAIAIE 388


Lambda     K      H
   0.318    0.132    0.376 

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: 527
Number of extensions: 16
Number of successful extensions: 2
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: 390
Length adjustment: 31
Effective length of query: 366
Effective length of database: 359
Effective search space:   131394
Effective search space used:   131394
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_010440841.1 G7G_RS0109505 (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.1129782.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   5.7e-127  409.7   7.4   6.6e-127  409.5   7.4    1.0  1  NCBI__GCF_000192475.1:WP_010440841.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000192475.1:WP_010440841.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  409.5   7.4  6.6e-127  6.6e-127       1     385 []       6     388 ..       6     388 .. 0.97

  Alignments for each domain:
  == domain 1  score: 409.5 bits;  conditional E-value: 6.6e-127
                             TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpes 73 
                                           i +a+Rtp+g ++g +  ++a+dL+ a+i+++l+ ag d   +dev +G+vl+ag+++++aR+a +aagl+e+
  NCBI__GCF_000192475.1:WP_010440841.1   6 IAGAARTPMGGFQGMFDGVTAADLGGAAIRAALKGAGAD--TVDEVLMGCVLPAGQGQAPARQAGFAAGLGEE 76 
                                           7899******99**********************98665..8******************************* PP

                             TIGR01930  74 vpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl.. 144
                                           vpa+t+n++C+Sg++A ++a ++i+ G+ +++vaGG+Esm+++p+ll++   r ++++g+ ++ d++  d+  
  NCBI__GCF_000192475.1:WP_010440841.1  77 VPATTLNKMCGSGMKAAMIAFDQIALGHTQTMVAGGMESMTNAPYLLPKM--RGGARIGHGQVVDHMFLDGle 147
                                           ************************************************97..899999999999999888889 PP

                             TIGR01930 145 ..vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegirp 213
                                              +++  mg+ Ae +a+ y+++Re qDeyalrS ++a +A+e++ f++ei+ v+++++  ++v++ De+++ 
  NCBI__GCF_000192475.1:WP_010440841.1 148 daYDKGRLMGTFAEDCAESYQFTREAQDEYALRSLSNALSAQENNAFDQEITSVSIQTRkgEVVLDADEQPQ- 219
                                           9888999**************************************************999888889999887. PP

                             TIGR01930 214 nttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgp 286
                                               ek+ +Lkpaf+e +g tvtA+Nss+++DGAaal+l+s e a++ +lt+ ari ++a  +  p  ++++p
  NCBI__GCF_000192475.1:WP_010440841.1 220 SARPEKIPTLKPAFRE-DG-TVTAANSSSISDGAAALVLASAEEAEKQNLTVRARILGHASHAQAPGLFTTAP 290
                                           8899**********96.9*.6**************************************************** PP

                             TIGR01930 287 vpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllke 359
                                           vpA +k+L++ g++ +d+dl+E+nEAFA++ +a+++e+g l++e vNvnGGA AlGHP+GasGari++tll++
  NCBI__GCF_000192475.1:WP_010440841.1 291 VPAAQKLLDRIGWKKEDVDLWEVNEAFAVVPMAFMHEMG-LSREIVNVNGGACALGHPIGASGARIMVTLLNA 362
                                           ***************************************.88******************************* PP

                             TIGR01930 360 LkergkkyGlatlCvggGqGaAvile 385
                                           L++r+ k+G+a++C+ggG G+A+ +e
  NCBI__GCF_000192475.1:WP_010440841.1 363 LEKRDLKRGVAAICIGGGEGTAIAIE 388
                                           **********************9987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (390 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: 15.55
//
[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 2024 update 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