Alignments for a candidate for fadA in Herbaspirillum seropedicae SmR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Herbaspirillum seropedicae SmR1

Align subunit of β-ketoadipyl CoA thiolase (EC 2.3.1.174; EC 2.3.1.16) (characterized)
to candidate HSERO_RS20660 HSERO_RS20660 acetyl-CoA acetyltransferase

Query= metacyc::MONOMER-3207
         (400 letters)



>FitnessBrowser__HerbieS:HSERO_RS20660
          Length = 401

 Score =  558 bits (1439), Expect = e-164
 Identities = 276/399 (69%), Positives = 332/399 (83%), Gaps = 1/399 (0%)

Query: 3   DVFICDAIRTPIGRFGGALAGVRADDLAAVPLKALIEPNPAVQWDQVDEVFFGCANQAGE 62
           +  ICDAIRTP GR+GGAL  VRADDLAA P+++L+E NP V W +V+++ +GCANQAGE
Sbjct: 2   EALICDAIRTPFGRYGGALGAVRADDLAAAPIRSLMERNPGVDWSRVEDILYGCANQAGE 61

Query: 63  DNRNVARMALLLAGLPESIPGVTLNRLCASGMDAIGTAFRAIASGEMELAIAGGVESMSR 122
           DNRNVARMA LLAGLP ++PG T+NRLC S +DA+G A RAI SGE++L IAGGVESM+R
Sbjct: 62  DNRNVARMAGLLAGLPIAVPGSTVNRLCGSSLDAVGMAARAIKSGEVQLMIAGGVESMTR 121

Query: 123 APFVMGKAESGYSRNMKLEDTTIGWRFINPLMKSQYGVDSMPETADNVADDYQVSRADQD 182
           APFVMGKAES ++R+  + DTTIGWRF+NPLMK+QYG+DSMPETA+NVA D+Q++RADQD
Sbjct: 122 APFVMGKAESAFARSAAIFDTTIGWRFVNPLMKAQYGIDSMPETAENVATDFQINRADQD 181

Query: 183 AFALRSQQKAAAAQAAGFFAEEIVPVRIAHKKGE-TIVERDEHLRPETTLEALTKLKPVN 241
           AFALRSQQ+ AAAQAAGFFA EI P+ I  KKG+  +V  DEH RP+TTL  L KLK V 
Sbjct: 182 AFALRSQQRWAAAQAAGFFAGEIAPLTIPQKKGDPLVVTTDEHPRPDTTLATLAKLKGVV 241

Query: 242 GPDKTVTAGNASGVNDGAAALILASAEAVKKHGLTPRARVLGMASGGVAPRVMGIGPVPA 301
            PD TVTAGNASGVNDGA AL+LAS +A   + L PRARVLGMA+ GVAPR+MG GP PA
Sbjct: 242 RPDGTVTAGNASGVNDGACALLLASPKAADLYRLKPRARVLGMATAGVAPRIMGFGPAPA 301

Query: 302 VRKLTERLGVAVSDFDVIELNEAFASQGLAVLRELGVADDAPQVNPNGGAIALGHPLGMS 361
           VRK+  ++G+ ++  DVIELNEAFA+QGLAV+R+LG+ DDA  VNPNGGAIA+GHPLG S
Sbjct: 302 VRKVLAQVGLTLAQMDVIELNEAFAAQGLAVMRDLGLPDDAAHVNPNGGAIAIGHPLGAS 361

Query: 362 GARLVLTALHQLEKSGGRKGLATMCVGVGQGLALAIERV 400
           GARLV TA++QLE+SGGR  L TMC+GVGQG+AL IERV
Sbjct: 362 GARLVTTAINQLERSGGRYALCTMCIGVGQGIALVIERV 400


Lambda     K      H
   0.318    0.134    0.383 

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: 549
Number of extensions: 16
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: 400
Length of database: 401
Length adjustment: 31
Effective length of query: 369
Effective length of database: 370
Effective search space:   136530
Effective search space used:   136530
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 HSERO_RS20660 HSERO_RS20660 (acetyl-CoA acetyltransferase)
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.25239.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   5.5e-136  439.4   1.5   6.2e-136  439.2   1.5    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS20660  HSERO_RS20660 acetyl-CoA acetylt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS20660  HSERO_RS20660 acetyl-CoA acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  439.2   1.5  6.2e-136  6.2e-136       1     385 []       5     398 ..       5     398 .. 0.95

  Alignments for each domain:
  == domain 1  score: 439.2 bits;  conditional E-value: 6.2e-136
                                  TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikellera.gldpekidevilGnvlqageq.aniaReaal 66 
                                                i da+Rtp+g++gg+l  ++a+dL+aa i++l+er+ g+d ++++++ +G++ qage+  n+aR+a l
  lcl|FitnessBrowser__HerbieS:HSERO_RS20660   5 ICDAIRTPFGRYGGALGAVRADDLAAAPIRSLMERNpGVDWSRVEDILYGCANQAGEDnRNVARMAGL 72 
                                                789*******99**********************************************9********* PP

                                  TIGR01930  67 aaglpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgka 134
                                                 aglp  vp+ tvnr+C+S+l+Av +aa++ik+Ge ++++aGGvEsm+r+p+++ ++   es+  ++a
  lcl|FitnessBrowser__HerbieS:HSERO_RS20660  73 LAGLPIAVPGSTVNRLCGSSLDAVGMAARAIKSGEVQLMIAGGVESMTRAPFVMGKA---ESAFARSA 137
                                                ****************************************************99997...34444444 PP

                                  TIGR01930 135 kledqllkdl..........vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkde 192
                                                   d+++  +          ++   sm etAen+a++++i+R +qD++alrS+q+ a+A+++g+f+ e
  lcl|FitnessBrowser__HerbieS:HSERO_RS20660 138 AIFDTTI--GwrfvnplmkaQYGIDSMPETAENVATDFQINRADQDAFALRSQQRWAAAQAAGFFAGE 203
                                                4444333..13457888897777789****************************************** PP

                                  TIGR01930 193 ivpvevkgk...kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseev 257
                                                i p+++++k   + vv++De++rp+ttl++LakLk + + ++g tvtAgN+s++nDGA+alll+s ++
  lcl|FitnessBrowser__HerbieS:HSERO_RS20660 204 IAPLTIPQKkgdPLVVTTDEHPRPDTTLATLAKLKGVVR-PDG-TVTAGNASGVNDGACALLLASPKA 269
                                                *******999*999************************9.69*.6*********************** PP

                                  TIGR01930 258 akelgltplarivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelg 325
                                                a+ + l+p ar+ ++a+agv p++mg+gp+pA++k+L++ gl++ ++d++E+nEAFAaq lav+++lg
  lcl|FitnessBrowser__HerbieS:HSERO_RS20660 270 ADLYRLKPRARVLGMATAGVAPRIMGFGPAPAVRKVLAQVGLTLAQMDVIELNEAFAAQGLAVMRDLG 337
                                                ******************************************************************** PP

                                  TIGR01930 326 sld.lekvNvnGGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                                + d  + vN nGGAiA+GHPlGasGar+v+t +++L++ g++y+l t+C+g GqG+A+++e
  lcl|FitnessBrowser__HerbieS:HSERO_RS20660 338 LPDdAAHVNPNGGAIAIGHPLGASGARLVTTAINQLERSGGRYALCTMCIGVGQGIALVIE 398
                                                855699*****************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (401 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: 00:00:00.01
# Mc/sec: 12.19
//
[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