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.3383.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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01
# Mc/sec: 8.53
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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:

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:

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:

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:

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