Alignments for a candidate for fadA in Herbaspirillum autotrophicum IAM 14942

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Herbaspirillum autotrophicum IAM 14942

Align Acetyl-CoA acetyltransferase; Acetoacetyl-CoA thiolase; Beta-ketothiolase; EC 2.3.1.9 (characterized)
to candidate WP_050461615.1 AKL27_RS04650 acetyl-CoA C-acetyltransferase

Query= SwissProt::P14611
         (393 letters)



>NCBI__GCF_001189915.1:WP_050461615.1
          Length = 391

 Score =  588 bits (1517), Expect = e-173
 Identities = 299/392 (76%), Positives = 338/392 (86%), Gaps = 1/392 (0%)

Query: 1   MTDVVIVSAARTAVGKFGGSLAKIPAPELGAVVIKAALERAGVKPEQVSEVIMGQVLTAG 60
           M DVVIV+A RTAVGKFGG+L+KI A +LGA VIK  L + G+KPEQ+SEVI+GQVLTAG
Sbjct: 1   MDDVVIVAAQRTAVGKFGGALSKIAASDLGAHVIKGLLAKTGIKPEQISEVILGQVLTAG 60

Query: 61  SGQNPARQAAIKAGLPAMVPAMTINKVCGSGLKAVMLAANAIMAGDAEIVVAGGQENMSA 120
            GQNPARQA I++GLP MVPA  + KVCGSGLKA+ LAA AI  GDA+IV+AGGQENMSA
Sbjct: 61  VGQNPARQAVIRSGLPDMVPAFVVGKVCGSGLKAIHLAAQAIKCGDAQIVIAGGQENMSA 120

Query: 121 APHVLPGSRDGFRMGDAKLVDTMIVDGLWDVYNQYHMGITAENVAKEYGITREAQDEFAV 180
           +PHVL  SRDGFRMGDAKL DTMIVDGLWDVYNQYHMGITAENVAK+Y I+R  QDEFAV
Sbjct: 121 SPHVLNHSRDGFRMGDAKLTDTMIVDGLWDVYNQYHMGITAENVAKKYEISRAEQDEFAV 180

Query: 181 GSQNKAEAAQKAGKFDEEIVPVLIPQRKGDPVAFKTDEFVRQGATLDSMSGLKPAFDKAG 240
            SQNKAEAAQKAGKF +EI+P  I  +KG  V   +DEF++ GATL+ M+GL+PAF K G
Sbjct: 181 ASQNKAEAAQKAGKFKDEILPYEIVTKKGTTVV-DSDEFIKHGATLEGMAGLRPAFAKDG 239

Query: 241 TVTAANASGLNDGAAAVVVMSAAKAKELGLTPLATIKSYANAGVDPKVMGMGPVPASKRA 300
           TVTA NASG+NDGAAAV+V SA  AKELGL  LA IKSY++AG+DP +MGMGPVPAS+  
Sbjct: 240 TVTAGNASGINDGAAAVIVTSARLAKELGLPVLAKIKSYSSAGLDPSIMGMGPVPASQLC 299

Query: 301 LSRAEWTPQDLDLMEINEAFAAQALAVHQQMGWDTSKVNVNGGAIAIGHPIGASGCRILV 360
           L +A WT QDLDLMEINEAFAAQA+AV++QMGWDTSK+NVNGGAIAIGHPIGASGCRILV
Sbjct: 300 LQKAGWTAQDLDLMEINEAFAAQAIAVNKQMGWDTSKINVNGGAIAIGHPIGASGCRILV 359

Query: 361 TLLHEMKRRDAKKGLASLCIGGGMGVALAVER 392
           TLLHEM RRDAK+GLASLCIGGGMGVALAVER
Sbjct: 360 TLLHEMARRDAKRGLASLCIGGGMGVALAVER 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: 528
Number of extensions: 20
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 WP_050461615.1 AKL27_RS04650 (acetyl-CoA C-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.3204880.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   4.6e-153  495.6   9.5   5.2e-153  495.5   9.5    1.0  1  NCBI__GCF_001189915.1:WP_050461615.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001189915.1:WP_050461615.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  495.5   9.5  5.2e-153  5.2e-153       1     385 []       6     390 ..       6     390 .. 0.99

  Alignments for each domain:
  == domain 1  score: 495.5 bits;  conditional E-value: 5.2e-153
                             TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpes 73 
                                           iv+a Rt++gk+gg+l+++ a+dL+a+vik+ll+++g++pe+i evilG+vl+ag ++n+aR+a++++glp+ 
  NCBI__GCF_001189915.1:WP_050461615.1   6 IVAAQRTAVGKFGGALSKIAASDLGAHVIKGLLAKTGIKPEQISEVILGQVLTAGVGQNPARQAVIRSGLPDM 78 
                                           8************************************************************************ PP

                             TIGR01930  74 vpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllkdl.. 144
                                           vpa+ v +vC+Sgl+A++laaq+ik+G+a++v+aGG E+mS +p++l++s  r+++++g+akl d+++ d+  
  NCBI__GCF_001189915.1:WP_050461615.1  79 VPAFVVGKVCGSGLKAIHLAAQAIKCGDAQIVIAGGQENMSASPHVLNHS--RDGFRMGDAKLTDTMIVDGlw 149
                                           ************************************************98..9*****************9** PP

                             TIGR01930 145 .vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvskDegirpn 214
                                            v+++++mg+tAen+akky+isR eqDe+a++S++ka++A+++gkfkdei+p+e+ +k  ++vv++De i+ +
  NCBI__GCF_001189915.1:WP_050461615.1 150 dVYNQYHMGITAENVAKKYEISRAEQDEFAVASQNKAEAAQKAGKFKDEILPYEIVTKkgTTVVDSDEFIKHG 222
                                           *99****************************************************9999999*********** PP

                             TIGR01930 215 ttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaavagvdpeemglgpv 287
                                            tle +a+L+paf++ +g tvtAgN+s++nDGAaa++++s + akelgl +la+i s++ ag+dp++mg+gpv
  NCBI__GCF_001189915.1:WP_050461615.1 223 ATLEGMAGLRPAFAK-DG-TVTAGNASGINDGAAAVIVTSARLAKELGLPVLAKIKSYSSAGLDPSIMGMGPV 293
                                           *************95.9*.6***************************************************** PP

                             TIGR01930 288 pAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHPlGasGarivltllkeL 360
                                           pA++ +L+kag++++d+dl+EinEAFAaq++av+k++g  d++k+NvnGGAiA+GHP+GasG+ri++tll+e+
  NCBI__GCF_001189915.1:WP_050461615.1 294 PASQLCLQKAGWTAQDLDLMEINEAFAAQAIAVNKQMG-WDTSKINVNGGAIAIGHPIGASGCRILVTLLHEM 365
                                           **************************************.88******************************** PP

                             TIGR01930 361 kergkkyGlatlCvggGqGaAvile 385
                                           ++r++k+Gla+lC+ggG+G+A+ +e
  NCBI__GCF_001189915.1:WP_050461615.1 366 ARRDAKRGLASLCIGGGMGVALAVE 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 15.39
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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:

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