Alignments for a candidate for fadA in Flavobacterium sp. LM5

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Flavobacterium sp. LM5

Align 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 (characterized)
to candidate WP_078211525.1 BXU11_RS06925 acetyl-CoA C-acyltransferase

Query= SwissProt::O32177
         (391 letters)



>NCBI__GCF_002017945.1:WP_078211525.1
          Length = 393

 Score =  387 bits (993), Expect = e-112
 Identities = 205/392 (52%), Positives = 264/392 (67%), Gaps = 2/392 (0%)

Query: 1   MKEAVIVSGARTPVGKAKKGSLATVRPDDLGAICVKETLKRAGGYEGN-IDDLIIGCATP 59
           MK A IV   RT VGKA KG     RPD+L A  ++  +     ++   IDD+++G A P
Sbjct: 1   MKTAYIVKAYRTAVGKAPKGVFRFKRPDELAAETIQYMMNELPDFDKTRIDDVMVGNAMP 60

Query: 60  EAEQGLNMARNIGALAGLPYTVPAITVNRYCSSGLQSIAYAAEKIMLGAYDTAIAGGAES 119
           EAEQGLN+ R I  +      VP +TVNRYC+SGL++I  A  KI  G     IAGGAES
Sbjct: 61  EAEQGLNVGRLISLMGLKVDDVPGVTVNRYCASGLETIGMATAKIQSGMAHCIIAGGAES 120

Query: 120 MSQVPMMGHVTRPNLALAEKAPE-YYMSMGHTAEQVAKKYGVSREDQDAFAVRSHQNAAK 178
           MS +PM G+   P+  +A    E YY  MG T+E VAK++ +SR DQD FA +SH  A K
Sbjct: 121 MSYIPMGGYKPTPDYKVAAAGHEDYYWGMGLTSEAVAKQFNISRADQDEFAFQSHNKALK 180

Query: 179 ALAEGKFKDEIVPVEVTVTEIGEDHKPMEKQFVFSQDEGVRPQTTADILSTLRPAFSVDG 238
           A AEGKF ++IVP+ V  T I E+ K   K +V ++DEG R  T+ + L+ LRP F+ DG
Sbjct: 181 AQAEGKFDNQIVPITVEQTFINENGKKETKSYVVTKDEGPRAGTSLEALAGLRPVFAADG 240

Query: 239 TVTAGNSSQTSDGAAAVMLMDREKADALGLAPLVKFRSFAVGGVPPEVMGIGPVEAIPRA 298
           +VTAGNSSQ SDGAA V++M  E    L + P+ +  +FA  GV P +MGIGPV+AIP+A
Sbjct: 241 SVTAGNSSQMSDGAAFVLVMSEEMVKELNIQPIARLVNFASAGVEPRIMGIGPVKAIPKA 300

Query: 299 LKLAGLQLQDIGLFELNEAFASQAIQVIRELGIDEEKVNVNGGAIALGHPLGCTGTKLTL 358
           LK AGL L DI L ELNEAFASQA+ V REL ++ + +NVNGGAIALGHPLGCTG KL++
Sbjct: 301 LKQAGLTLNDIDLIELNEAFASQALAVTRELNLNPDIINVNGGAIALGHPLGCTGAKLSV 360

Query: 359 SLIHEMKRRNEQFGVVTMCIGGGMGAAGVFEL 390
            L  EMKRR  ++G+V+MC+G G G+AG+FEL
Sbjct: 361 QLFDEMKRRGNKYGIVSMCVGTGQGSAGIFEL 392


Lambda     K      H
   0.316    0.133    0.377 

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: 420
Number of extensions: 13
Number of successful extensions: 3
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: 391
Length of database: 393
Length adjustment: 31
Effective length of query: 360
Effective length of database: 362
Effective search space:   130320
Effective search space used:   130320
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate WP_078211525.1 BXU11_RS06925 (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.2433198.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   9.4e-139  448.5   1.0   1.1e-138  448.3   1.0    1.0  1  NCBI__GCF_002017945.1:WP_078211525.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002017945.1:WP_078211525.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  448.3   1.0  1.1e-138  1.1e-138       1     385 []       6     391 ..       6     391 .. 0.97

  Alignments for each domain:
  == domain 1  score: 448.3 bits;  conditional E-value: 1.1e-138
                             TIGR01930   1 ivdavRtpig.klggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.aniaReaalaagl 70 
                                           iv+a+Rt++g + +g+++  ++++L+a++i+ +++   ++d+ +id+v++Gn+++++eq  n++R + l    
  NCBI__GCF_002017945.1:WP_078211525.1   6 IVKAYRTAVGkAPKGVFRFKRPDELAAETIQYMMNELpDFDKTRIDDVMVGNAMPEAEQgLNVGRLISLMGLK 78 
                                           89********988******************************************************998777 PP

                             TIGR01930  71 pesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkd 143
                                            ++vp++tvnr+CaSgl+++ +a +ki++G+a +++aGG+EsmS +p++  +   + ++k+ +a  ed     
  NCBI__GCF_002017945.1:WP_078211525.1  79 VDDVPGVTVNRYCASGLETIGMATAKIQSGMAHCIIAGGAESMSYIPMGGYKP--TPDYKVAAAGHED----- 144
                                           789**********************************************9998..7899988888887..... PP

                             TIGR01930 144 lvktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk...........kkvv 205
                                                  mg t+e +ak+++isR +qDe+a +Sh+ka kA++egkf+++ivp++v+++           + vv
  NCBI__GCF_002017945.1:WP_078211525.1 145 ---YYWGMGLTSEAVAKQFNISRADQDEFAFQSHNKALKAQAEGKFDNQIVPITVEQTfinengkketkSYVV 214
                                           ...4699*************************************************99*******99988899 PP

                             TIGR01930 206 skDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvd 278
                                           +kDeg+r++t+le+La+L+p+f+  +gs vtAgNssq++DGAa++l+msee++kel+++p+ar+v++a agv+
  NCBI__GCF_002017945.1:WP_078211525.1 215 TKDEGPRAGTSLEALAGLRPVFAA-DGS-VTAGNSSQMSDGAAFVLVMSEEMVKELNIQPIARLVNFASAGVE 285
                                           **********************95.9*7.******************************************** PP

                             TIGR01930 279 peemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGar 351
                                           p++mg+gpv+Ai+kaLk+agl+++didl+E+nEAFA+q+lav++el+ l+++ +NvnGGAiAlGHPlG++Ga 
  NCBI__GCF_002017945.1:WP_078211525.1 286 PRIMGIGPVKAIPKALKQAGLTLNDIDLIELNEAFASQALAVTRELN-LNPDIINVNGGAIALGHPLGCTGAK 357
                                           ***********************************************.88*********************** PP

                             TIGR01930 352 ivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                           + ++l++e+k+rg kyG++++Cvg+GqG+A i+e
  NCBI__GCF_002017945.1:WP_078211525.1 358 LSVQLFDEMKRRGNKYGIVSMCVGTGQGSAGIFE 391
                                           *******************************997 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (393 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 18.26
//
[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