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 Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate HSERO_RS01180 HSERO_RS01180 acetyl-CoA acetyltransferase

Query= SwissProt::P14611
         (393 letters)



>FitnessBrowser__HerbieS:HSERO_RS01180
          Length = 391

 Score =  591 bits (1524), Expect = e-173
 Identities = 298/392 (76%), Positives = 339/392 (86%), Gaps = 1/392 (0%)

Query: 1   MTDVVIVSAARTAVGKFGGSLAKIPAPELGAVVIKAALERAGVKPEQVSEVIMGQVLTAG 60
           M DVVIV+A RTA+GKFGG+L+KI A +LGA VIKA L + G+KPE +SEVI+GQVLTAG
Sbjct: 1   MDDVVIVAAQRTAIGKFGGALSKIAAADLGAQVIKALLAKTGIKPEAISEVILGQVLTAG 60

Query: 61  SGQNPARQAAIKAGLPAMVPAMTINKVCGSGLKAVMLAANAIMAGDAEIVVAGGQENMSA 120
            GQNPARQ+ IK+GLP MVPA  + KVCGSGLKAV LAA AI  GDA+IV+AGGQENMSA
Sbjct: 61  LGQNPARQSVIKSGLPDMVPAFVVGKVCGSGLKAVQLAAQAIRCGDAQIVIAGGQENMSA 120

Query: 121 APHVLPGSRDGFRMGDAKLVDTMIVDGLWDVYNQYHMGITAENVAKEYGITREAQDEFAV 180
           +PHVL  SRDGFRMGDAKL DTMIVDGLWDVYNQYHMGITAENVAK++ I+RE QD FA 
Sbjct: 121 SPHVLNNSRDGFRMGDAKLTDTMIVDGLWDVYNQYHMGITAENVAKKFEISREEQDAFAA 180

Query: 181 GSQNKAEAAQKAGKFDEEIVPVLIPQRKGDPVAFKTDEFVRQGATLDSMSGLKPAFDKAG 240
            SQNKAEAAQKAGKF +EIVP+ I  +K + V F TDEFV+ G T +S++ L+PAFDKAG
Sbjct: 181 ASQNKAEAAQKAGKFKDEIVPIEIKGKK-ETVVFDTDEFVKHGVTAESLATLRPAFDKAG 239

Query: 241 TVTAANASGLNDGAAAVVVMSAAKAKELGLTPLATIKSYANAGVDPKVMGMGPVPASKRA 300
           TVTA NASG+NDGAAAVVV SA  A ELGL  LA IK+Y++AG+DP +MGMGPVPAS+  
Sbjct: 240 TVTAGNASGINDGAAAVVVTSAKLAAELGLPVLAKIKAYSSAGLDPSIMGMGPVPASQLT 299

Query: 301 LSRAEWTPQDLDLMEINEAFAAQALAVHQQMGWDTSKVNVNGGAIAIGHPIGASGCRILV 360
           L +A WTPQDLDLMEINEAFAAQA+AV++QMGWDTSK+NVNGGAIA+GHPIGASGCR+LV
Sbjct: 300 LKKAGWTPQDLDLMEINEAFAAQAIAVNKQMGWDTSKINVNGGAIALGHPIGASGCRVLV 359

Query: 361 TLLHEMKRRDAKKGLASLCIGGGMGVALAVER 392
           TLLHEM RRDAKKGLASLCIGGGMGVALAVER
Sbjct: 360 TLLHEMVRRDAKKGLASLCIGGGMGVALAVER 391


Lambda     K      H
   0.315    0.131    0.369 

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: 529
Number of extensions: 18
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: 393
Length of database: 391
Length adjustment: 31
Effective length of query: 362
Effective length of database: 360
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 HSERO_RS01180 HSERO_RS01180 (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.29264.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                  -----------
   3.1e-152  492.9  10.6   3.5e-152  492.7  10.6    1.0  1  lcl|FitnessBrowser__HerbieS:HSERO_RS01180  HSERO_RS01180 acetyl-CoA acetylt


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__HerbieS:HSERO_RS01180  HSERO_RS01180 acetyl-CoA acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  492.7  10.6  3.5e-152  3.5e-152       1     385 []       6     390 ..       6     390 .. 0.99

  Alignments for each domain:
  == domain 1  score: 492.7 bits;  conditional E-value: 3.5e-152
                                  TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaa 68 
                                                iv+a Rt+igk+gg+l+++ a+dL+a+vik+ll+++g++pe+i evilG+vl+ag ++n+aR+ ++++
  lcl|FitnessBrowser__HerbieS:HSERO_RS01180   6 IVAAQRTAIGKFGGALSKIAAADLGAQVIKALLAKTGIKPEAISEVILGQVLTAGLGQNPARQSVIKS 73 
                                                8******************************************************************* PP

                                  TIGR01930  69 glpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakl 136
                                                glp+ vpa+ v +vC+Sgl+Av+laaq+i++G+a++v+aGG E+mS +p++l++s  r+++++g+akl
  lcl|FitnessBrowser__HerbieS:HSERO_RS01180  74 GLPDMVPAFVVGKVCGSGLKAVQLAAQAIRCGDAQIVIAGGQENMSASPHVLNNS--RDGFRMGDAKL 139
                                                *****************************************************98..9********** PP

                                  TIGR01930 137 edqllkdl...vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk 201
                                                 d+++ d+   v+++++mg+tAen+akk++isReeqD++a++S++ka++A+++gkfkdeivp+e+kgk
  lcl|FitnessBrowser__HerbieS:HSERO_RS01180 140 TDTMIVDGlwdVYNQYHMGITAENVAKKFEISREEQDAFAAASQNKAEAAQKAGKFKDEIVPIEIKGK 207
                                                *******9***99******************************************************9 PP

                                  TIGR01930 202 ..kkvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltpla 267
                                                  ++v+++De ++ ++t+e+La+L+paf++ +g tvtAgN+s++nDGAaa++++s + a+elgl +la
  lcl|FitnessBrowser__HerbieS:HSERO_RS01180 208 keTVVFDTDEFVKHGVTAESLATLRPAFDK-AG-TVTAGNASGINDGAAAVVVTSAKLAAELGLPVLA 273
                                                99999***********************95.9*.6********************************* PP

                                  TIGR01930 268 rivsaavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvn 335
                                                +i +++ ag+dp++mg+gpvpA++  Lkkag++ +d+dl+EinEAFAaq++av+k++g  d++k+Nvn
  lcl|FitnessBrowser__HerbieS:HSERO_RS01180 274 KIKAYSSAGLDPSIMGMGPVPASQLTLKKAGWTPQDLDLMEINEAFAAQAIAVNKQMG-WDTSKINVN 340
                                                **********************************************************.88******* PP

                                  TIGR01930 336 GGAiAlGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                                GGAiAlGHP+GasG+r+++tll+e+ +r++k Gla+lC+ggG+G+A+ +e
  lcl|FitnessBrowser__HerbieS:HSERO_RS01180 341 GGAIALGHPIGASGCRVLVTLLHEMVRRDAKKGLASLCIGGGMGVALAVE 390
                                                **********************************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (391 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: 00:00:00.02
# Mc/sec: 7.49
//
[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