Alignments for a candidate for fadA in Azorhizobium caulinodans ORS 571

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Azorhizobium caulinodans ORS 571

Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_043879632.1 AZC_RS20025 acetyl-CoA C-acyltransferase

Query= BRENDA::P45359
         (392 letters)



>NCBI__GCF_000010525.1:WP_043879632.1
          Length = 393

 Score =  406 bits (1043), Expect = e-118
 Identities = 200/389 (51%), Positives = 273/389 (70%)

Query: 2   KEVVIASAVRTAIGSYGKSLKDVPAVDLGATAIKEAVKKAGIKPEDVNEVILGNVLQAGL 61
           +++VIA  VRTAIG+Y  +LK  PA DLGA  ++E V++AG+ P  V  V++GNV+QAG 
Sbjct: 3   RDIVIAHPVRTAIGAYNGTLKGTPATDLGAVVVRETVRRAGLDPAAVGSVVMGNVIQAGN 62

Query: 62  GQNPARQASFKAGLPVEIPAMTINKVCGSGLRTVSLAAQIIKAGDADVIIAGGMENMSRA 121
             NPARQAS   GLPVE+PAMT+N+VCGSG + V  AA  I +G  DV +AGGMENM RA
Sbjct: 63  RMNPARQASIHGGLPVEVPAMTVNRVCGSGAQAVVTAALEIASGLHDVAVAGGMENMDRA 122

Query: 122 PYLANNARWGYRMGNAKFVDEMITDGLWDAFNDYHMGITAENIAERWNISREEQDEFALA 181
           PYL +  RWGYRMG A+ +D M+TDGL DAF+  H G   E++  R  I+R EQD FA  
Sbjct: 123 PYLMDGGRWGYRMGPAQILDSMLTDGLNDAFSGSHSGWHTEDLVARSQITRAEQDAFAAR 182

Query: 182 SQKKAEEAIKSGQFKDEIVPVVIKGRKGETVVDTDEHPRFGSTIEGLAKLKPAFKKDGTV 241
           SQ++   A   G+F +EIV V +KGRKG  +   DE PR  +T+E LA+L+PAF+ +GT+
Sbjct: 183 SQQRFAAAQAEGRFTEEIVAVEVKGRKGIELFSVDEAPRPDTTVETLARLRPAFRPEGTI 242

Query: 242 TAGNASGLNDCAAVLVIMSAEKAKELGVKPLAKIVSYGSAGVDPAIMGYGPFYATKAAIE 301
           TAGNA GLN  AA +++     A++ G+ PL ++  +G AGV+P + G GP  A + A++
Sbjct: 243 TAGNAPGLNSAAAAMIVAERAFAEKSGIAPLGRLAGFGIAGVEPGLFGLGPVPAVRKALQ 302

Query: 302 KAGWTVDELDLIESNEAFAAQSLAVAKDLKFDMNKVNVNGGAIALGHPIGASGARILVTL 361
            AGW++ +++ IE NEAFAA  +AVA++L    + VNV GGA+A GHPIGA+GA ++  L
Sbjct: 303 HAGWSLGDIERIEINEAFAAVPIAVARELGLPEDIVNVEGGAVAHGHPIGATGAILVTRL 362

Query: 362 VHAMQKRDAKKGLATLCIGGGQGTAILLE 390
           +HAM++   K+G+ TLCIGGGQG A+ LE
Sbjct: 363 LHAMKRDGVKRGVVTLCIGGGQGIALALE 391


Lambda     K      H
   0.315    0.132    0.375 

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: 475
Number of extensions: 17
Number of successful extensions: 1
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: 392
Length of database: 393
Length adjustment: 31
Effective length of query: 361
Effective length of database: 362
Effective search space:   130682
Effective search space used:   130682
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_043879632.1 AZC_RS20025 (acetyl-CoA C-acyltransferase)
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.8776.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   3.4e-133  430.2   2.7     4e-133  430.0   2.7    1.0  1  lcl|NCBI__GCF_000010525.1:WP_043879632.1  AZC_RS20025 acetyl-CoA C-acyltra


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000010525.1:WP_043879632.1  AZC_RS20025 acetyl-CoA C-acyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  430.0   2.7    4e-133    4e-133       2     385 .]       8     391 ..       7     391 .. 0.98

  Alignments for each domain:
  == domain 1  score: 430.0 bits;  conditional E-value: 4e-133
                                 TIGR01930   2 vdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaagl 70 
                                                  vRt+ig+++g+lk ++a dL+a v++e ++ragldp+++  v++Gnv+qag+ +n+aR+a +  gl
  lcl|NCBI__GCF_000010525.1:WP_043879632.1   8 AHPVRTAIGAYNGTLKGTPATDLGAVVVRETVRRAGLDPAAVGSVVMGNVIQAGNRMNPARQASIHGGL 76 
                                               5669*****99********************************************************** PP

                                 TIGR01930  71 pesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledq 139
                                               p +vpa+tvnrvC+Sg qAv +aa +i++G  dv+vaGG+E+m r+p+l++    r+++++g a+  d+
  lcl|NCBI__GCF_000010525.1:WP_043879632.1  77 PVEVPAMTVNRVCGSGAQAVVTAALEIASGLHDVAVAGGMENMDRAPYLMDGG--RWGYRMGPAQILDS 143
                                               **************************************************997..9************* PP

                                 TIGR01930 140 llkdl...vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kk 203
                                               +l d+   + ++ + g ++e l ++ +i+R eqD++a+rS+q+ a+A++eg+f +eiv vevkg+   +
  lcl|NCBI__GCF_000010525.1:WP_043879632.1 144 MLTDGlndAFSGSHSGWHTEDLVARSQITRAEQDAFAARSQQRFAAAQAEGRFTEEIVAVEVKGRkgIE 212
                                               *****99988999***************************************************99999 PP

                                 TIGR01930 204 vvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsa 272
                                                +s De +rp+tt+e+La+L+paf+ ++g t+tAgN+ +ln +Aaa++++++++a++ g+ pl+r+ ++
  lcl|NCBI__GCF_000010525.1:WP_043879632.1 213 LFSVDEAPRPDTTVETLARLRPAFR-PEG-TITAGNAPGLNSAAAAMIVAERAFAEKSGIAPLGRLAGF 279
                                               9***********************9.59*.6************************************** PP

                                 TIGR01930 273 avagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAl 341
                                               ++agv+p  +glgpvpA++kaL++ag+s+ di+ +EinEAFAa+ +av++elg l ++ vNv GGA+A 
  lcl|NCBI__GCF_000010525.1:WP_043879632.1 280 GIAGVEPGLFGLGPVPAVRKALQHAGWSLGDIERIEINEAFAAVPIAVARELG-LPEDIVNVEGGAVAH 347
                                               *****************************************************.88************* PP

                                 TIGR01930 342 GHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                               GHP+Ga+Ga++v++ll+++k++g+k+G++tlC+ggGqG+A+ le
  lcl|NCBI__GCF_000010525.1:WP_043879632.1 348 GHPIGATGAILVTRLLHAMKRDGVKRGVVTLCIGGGQGIALALE 391
                                               ****************************************9886 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (393 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 12.26
//
[ok]

This GapMind analysis is from Sep 24 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