Alignments for a candidate for fadA in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Shewanella loihica PV-4

Align 3-ketoacyl-CoA thiolase; Acetyl-CoA acyltransferase; Beta-ketothiolase; EC 2.3.1.16 (characterized)
to candidate 5210417 Shew_2858 acetyl-CoA acetyltransferase (RefSeq)

Query= SwissProt::O32177
         (391 letters)



>FitnessBrowser__PV4:5210417
          Length = 394

 Score =  315 bits (808), Expect = 1e-90
 Identities = 182/394 (46%), Positives = 242/394 (61%), Gaps = 5/394 (1%)

Query: 1   MKEAVIVSGARTPVGKAKKGSLATVRPDDLGAICVKETLKRAGGYEGNIDDLIIGCATPE 60
           M+EAVIVS ART + K+ +GSL   +   +   C+K+ ++RAG   G IDD I+G     
Sbjct: 1   MREAVIVSTARTGMAKSFRGSLNNTKSPTMLGHCIKQAVQRAGVEGGEIDDAIMGTVLTA 60

Query: 61  AEQGLNMARNIGALAGLPYTVPAITVNRYCSSGLQSIAYAAEKIMLGAYDTAIAGGAESM 120
              G+N+ARN    AGLP TV A T++R CSSGL +I  AA++I++      +AGG E++
Sbjct: 61  GTAGMNIARNAVLAAGLPNTVSAQTIDRQCSSGLMAIGMAAKQIIVDQQQIVVAGGQENI 120

Query: 121 SQVP---MMGHVTRPNLALAEKAPEYYMSMGHTAEQVAKKYGVSREDQDAFAVRSHQNAA 177
           + V    M       +  + +  P  YM M  TAE VAK YGVSRE QD +A+ S Q  A
Sbjct: 121 TAVQNEYMKWAADNADPNVMQFEPHAYMPMLKTAEHVAKVYGVSREAQDIYALMSQQRTA 180

Query: 178 KALAEGKFKDEIVPVEVTVTEIGEDHKPME-KQFVFSQDEGVRPQTTADILSTLRPAFSV 236
            A   G F DEIVP   T+     + K +  +Q    +DE  RP TT + L  L P    
Sbjct: 181 AAQEAGYFDDEIVPFTTTMAIQDRETKAISYQQVTLDRDECNRPSTTMESLQNLAPVIE- 239

Query: 237 DGTVTAGNSSQTSDGAAAVMLMDREKADALGLAPLVKFRSFAVGGVPPEVMGIGPVEAIP 296
            G +TAGN+SQ SDGA+A ++M+R+ A+  GLAPL  +R  AV G  PE MGIGP+ AIP
Sbjct: 240 GGFITAGNASQLSDGASACVVMERKLAEQRGLAPLGIYRGIAVAGCAPEEMGIGPIYAIP 299

Query: 297 RALKLAGLQLQDIGLFELNEAFASQAIQVIRELGIDEEKVNVNGGAIALGHPLGCTGTKL 356
           + LK  GL + DIGL+E+NEAFA QA+     LGID  + NVNGG I++GHP G TG++L
Sbjct: 300 KLLKQHGLTIDDIGLWEINEAFAVQALYCRDHLGIDPARYNVNGGGISIGHPYGMTGSRL 359

Query: 357 TLSLIHEMKRRNEQFGVVTMCIGGGMGAAGVFEL 390
               + E KRR  ++ VV MCIGGGMGAAG+FE+
Sbjct: 360 VGHALIEGKRRGVKYVVVGMCIGGGMGAAGLFEV 393


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: 408
Number of extensions: 14
Number of successful extensions: 4
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: 394
Length adjustment: 31
Effective length of query: 360
Effective length of database: 363
Effective search space:   130680
Effective search space used:   130680
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 5210417 Shew_2858 (acetyl-CoA acetyltransferase (RefSeq))
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.29457.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                        -----------
   4.2e-125  403.6   6.2   4.8e-125  403.4   6.2    1.0  1  lcl|FitnessBrowser__PV4:5210417  Shew_2858 acetyl-CoA acetyltrans


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5210417  Shew_2858 acetyl-CoA acetyltransferase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  403.4   6.2  4.8e-125  4.8e-125       1     385 []       6     392 ..       6     392 .. 0.96

  Alignments for each domain:
  == domain 1  score: 403.4 bits;  conditional E-value: 4.8e-125
                        TIGR01930   1 ivdavRtpig.klggslkelsaedLlaavikelleragldpekidevilGnvlqageq.aniaReaalaaglpesvpa 76 
                                      iv+++Rt ++ +++gsl+++++ ++l + ik++++rag++  +id++i+G+vl+ag+  +niaR+a+laaglp++v+a
  lcl|FitnessBrowser__PV4:5210417   6 IVSTARTGMAkSFRGSLNNTKSPTMLGHCIKQAVQRAGVEGGEIDDAIMGTVLTAGTAgMNIARNAVLAAGLPNTVSA 83 
                                      89********99****************************************************************** PP

                        TIGR01930  77 ltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdlvktklsmget 154
                                       t++r+C+Sgl A+ +aa++i + ++++vvaGG E+++ v    ++  ++++++++ ++ e        ++ ++m +t
  lcl|FitnessBrowser__PV4:5210417  84 QTIDRQCSSGLMAIGMAAKQIIVDQQQIVVAGGQENITAVQNEYMK-WAADNADPNVMQFEP-------HAYMPMLKT 153
                                      **************************************99866555.367777776666666.......7889***** PP

                        TIGR01930 155 AenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk............kkvvskDegirpnttlekL 220
                                      Ae++ak yg+sRe qD yal S+q++a+A+e+g+f+deivp++   +            ++++++De+ rp tt+e+L
  lcl|FitnessBrowser__PV4:5210417 154 AEHVAKVYGVSREAQDIYALMSQQRTAAAQEAGYFDDEIVPFTTTMAiqdretkaisyqQVTLDRDECNRPSTTMESL 231
                                      *****************************************9988778889*******999***************** PP

                        TIGR01930 221 akLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpvpAiekaLkkag 298
                                      ++L p+ +   g  +tAgN+sql+DGA+a ++m+++ a++ gl pl+ ++++avag+ peemg+gp++Ai+k+Lk++g
  lcl|FitnessBrowser__PV4:5210417 232 QNLAPVIE--GG-FITAGNASQLSDGASACVVMERKLAEQRGLAPLGIYRGIAVAGCAPEEMGIGPIYAIPKLLKQHG 306
                                      *******7..58.6**************************************************************** PP

                        TIGR01930 299 lsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvgg 376
                                      l+i+di l+EinEAFA+q+l+++++lg +d++++NvnGG i++GHP+G++G+r+v + l e k+rg+ky ++ +C+gg
  lcl|FitnessBrowser__PV4:5210417 307 LTIDDIGLWEINEAFAVQALYCRDHLG-IDPARYNVNGGGISIGHPYGMTGSRLVGHALIEGKRRGVKYVVVGMCIGG 383
                                      ***************************.88************************************************ PP

                        TIGR01930 377 GqGaAvile 385
                                      G+GaA ++e
  lcl|FitnessBrowser__PV4:5210417 384 GMGAAGLFE 392
                                      *****9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (394 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 9.41
//
[ok]

This GapMind analysis is from Sep 17 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