Alignments for a candidate for fadA in Methylobacterium nodulans ORS 2060

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Methylobacterium nodulans ORS 2060

Align acetyl-CoA C-acetyltransferase (EC 2.3.1.9) (characterized)
to candidate WP_043749977.1 MNOD_RS35365 acetyl-CoA C-acetyltransferase

Query= BRENDA::P45359
         (392 letters)



>NCBI__GCF_000022085.1:WP_043749977.1
          Length = 394

 Score =  410 bits (1054), Expect = e-119
 Identities = 200/390 (51%), Positives = 277/390 (71%)

Query: 1   MKEVVIASAVRTAIGSYGKSLKDVPAVDLGATAIKEAVKKAGIKPEDVNEVILGNVLQAG 60
           M ++V+   VRTAIG+Y  SLK +PA DLGA  ++E +++AG+ P +V  V++GNV+QAG
Sbjct: 3   MTDIVLCQPVRTAIGAYNGSLKGIPATDLGAVVVRETLRRAGLDPAEVGSVVMGNVVQAG 62

Query: 61  LGQNPARQASFKAGLPVEIPAMTINKVCGSGLRTVSLAAQIIKAGDADVIIAGGMENMSR 120
              NPARQA+   G PV +PA+T+N+VCGSG + +  AAQ I +G+ ++ +AGGMENM R
Sbjct: 63  NRMNPARQAAIGGGAPVSVPALTVNRVCGSGAQAIVTAAQQIVSGEVEIAVAGGMENMDR 122

Query: 121 APYLANNARWGYRMGNAKFVDEMITDGLWDAFNDYHMGITAENIAERWNISREEQDEFAL 180
           APYL    RWGYRMG A+ +D M+TDGL DAF+  H G   +++A R  ++RE QD FA 
Sbjct: 123 APYLLEGGRWGYRMGPAQILDSMLTDGLNDAFSGEHSGWHTDDLAARCQLTREAQDRFAA 182

Query: 181 ASQKKAEEAIKSGQFKDEIVPVVIKGRKGETVVDTDEHPRFGSTIEGLAKLKPAFKKDGT 240
            SQ++   A  +G F+ EIVPV IKGRKG     TDE PR  +T+E LA+LKPAF+KDGT
Sbjct: 183 RSQQRFAAAQAAGAFEAEIVPVEIKGRKGPETFATDEAPRPDTTMEILARLKPAFRKDGT 242

Query: 241 VTAGNASGLNDCAAVLVIMSAEKAKELGVKPLAKIVSYGSAGVDPAIMGYGPFYATKAAI 300
           +TAGNA GLN  AA +++ +   A+  G+ PL ++V+YG A V+P + G GP  A + A+
Sbjct: 243 ITAGNAPGLNSGAAAMIVAARGTAEARGIAPLGRLVAYGIAAVEPGLFGLGPVPAIRRAM 302

Query: 301 EKAGWTVDELDLIESNEAFAAQSLAVAKDLKFDMNKVNVNGGAIALGHPIGASGARILVT 360
           E+AGWT+ +++ IE NEAFAA  LAVA++L    + +NV GGAIA GHPIGA+GA +   
Sbjct: 303 ERAGWTLAQVERIEINEAFAAVPLAVAQELGLPEDIINVEGGAIAHGHPIGATGAVLTTR 362

Query: 361 LVHAMQKRDAKKGLATLCIGGGQGTAILLE 390
           L+H+M++   ++G+ TLCIGGGQG A+ LE
Sbjct: 363 LLHSMRRDGLRRGVVTLCIGGGQGIALALE 392


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: 456
Number of extensions: 14
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: 394
Length adjustment: 31
Effective length of query: 361
Effective length of database: 363
Effective search space:   131043
Effective search space used:   131043
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_043749977.1 MNOD_RS35365 (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.12145.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.9e-134  432.5   2.9     8e-134  432.3   2.9    1.0  1  lcl|NCBI__GCF_000022085.1:WP_043749977.1  MNOD_RS35365 acetyl-CoA C-acetyl


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000022085.1:WP_043749977.1  MNOD_RS35365 acetyl-CoA C-acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  432.3   2.9    8e-134    8e-134       5     385 .]      12     392 ..       8     392 .. 0.98

  Alignments for each domain:
  == domain 1  score: 432.3 bits;  conditional E-value: 8e-134
                                 TIGR01930   5 vRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaaglpes 73 
                                               vRt+ig+++gslk ++a dL+a v++e l+ragldp+++  v++Gnv+qag+ +n+aR+aa+  g p s
  lcl|NCBI__GCF_000022085.1:WP_043749977.1  12 VRTAIGAYNGSLKGIPATDLGAVVVRETLRRAGLDPAEVGSVVMGNVVQAGNRMNPARQAAIGGGAPVS 80 
                                               8*****99************************************************************* PP

                                 TIGR01930  74 vpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakledqllk 142
                                               vpaltvnrvC+Sg qA+ +aaq+i +Ge +++vaGG+E+m r+p+ll+    r+++++g a+  d++l 
  lcl|NCBI__GCF_000022085.1:WP_043749977.1  81 VPALTVNRVCGSGAQAIVTAAQQIVSGEVEIAVAGGMENMDRAPYLLEGG--RWGYRMGPAQILDSMLT 147
                                               ************************************************97..9**************** PP

                                 TIGR01930 143 dl...vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..kkvvs 206
                                               d+   + ++ + g +++ la++ +++Re qD++a+rS+q+ a+A+++g f++eivpve+kg+  +++++
  lcl|NCBI__GCF_000022085.1:WP_043749977.1 148 DGlndAFSGEHSGWHTDDLAARCQLTREAQDRFAARSQQRFAAAQAAGAFEAEIVPVEIKGRkgPETFA 216
                                               **9998899************************************************************ PP

                                 TIGR01930 207 kDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivsaava 275
                                               +De +rp+tt+e La+Lkpaf++ +g t+tAgN+ +ln GAaa++++ + +a++ g+ pl+r+v++++a
  lcl|NCBI__GCF_000022085.1:WP_043749977.1 217 TDEAPRPDTTMEILARLKPAFRK-DG-TITAGNAPGLNSGAAAMIVAARGTAEARGIAPLGRLVAYGIA 283
                                               *********************95.9*.6***************************************** PP

                                 TIGR01930 276 gvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiAlGHP 344
                                               +v+p  +glgpvpAi++a+++ag+++ +++ +EinEAFAa+ lav++elg l ++ +Nv GGAiA GHP
  lcl|NCBI__GCF_000022085.1:WP_043749977.1 284 AVEPGLFGLGPVPAIRRAMERAGWTLAQVERIEINEAFAAVPLAVAQELG-LPEDIINVEGGAIAHGHP 351
                                               **************************************************.88**************** PP

                                 TIGR01930 345 lGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                               +Ga+Ga ++++ll++++++g ++G++tlC+ggGqG+A+ le
  lcl|NCBI__GCF_000022085.1:WP_043749977.1 352 IGATGAVLTTRLLHSMRRDGLRRGVVTLCIGGGQGIALALE 392
                                               *************************************9886 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 9.72
//
[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