Alignments for a candidate for fadA in Mesorhizobium ciceri WSM1271

GapMind for catabolism of small carbon sources

Alignments for a candidate for fadA in Mesorhizobium ciceri WSM1271

Align acetyl-CoA:acetyl-CoA C-acetyltransferase / acetyl-CoA:propanoyl-CoA 2-C-acetyltransferase (EC 2.3.1.9; EC 2.3.1.16) (characterized)
to candidate YP_004140539.1 Mesci_1329 acetyl-CoA acetyltransferase

Query= reanno::Phaeo:GFF329
         (391 letters)



>NCBI__GCF_000185905.1:YP_004140539.1
          Length = 392

 Score =  605 bits (1560), Expect = e-178
 Identities = 301/387 (77%), Positives = 338/387 (87%)

Query: 3   NVVIASAARTAVGSFGGAFAKTPAHDLGAAVLQAVVERAGIDKSEVSETILGQVLTAAQG 62
           ++VIASAART VGSF GAFA TPAH+LGA V++ ++ RAG++  EV E ILGQVLTAAQG
Sbjct: 4   SIVIASAARTPVGSFNGAFAATPAHELGAVVIRELLSRAGVEPGEVDEVILGQVLTAAQG 63

Query: 63  QNPARQAHINAGLPQESAAWSLNQVCGSGLRAVALAAQHIQLGDAAIVCAGGQENMTLSP 122
           QNPARQA INAGLP+E+ AW LNQVCGSGLRA+AL  Q I +GDA ++ AGGQE+M+LS 
Sbjct: 64  QNPARQASINAGLPKETTAWGLNQVCGSGLRAIALGMQQIAIGDARVIIAGGQESMSLST 123

Query: 123 HAANLRAGHKMGDMSYIDTMIRDGLWDAFNGYHMGQTAENVAEKWQISREMQDEFAVASQ 182
           HA +LRAG KMGD   IDTMI+DGLWDAFNGYHMG TAENVA ++QI+RE QD+FA+ASQ
Sbjct: 124 HAQHLRAGVKMGDFKLIDTMIKDGLWDAFNGYHMGNTAENVARQFQITREDQDQFALASQ 183

Query: 183 NKAEAAQKAGKFADEIAAFTVKTRKGDIIVDQDEYIRHGATIEAMQKLRPAFAKDGSVTA 242
           NKAEAAQKAGKF DEI A T+K +KGD IVDQDEYIRHGATI+AM KL+PAF KDG+VTA
Sbjct: 184 NKAEAAQKAGKFKDEIVAVTIKGKKGDTIVDQDEYIRHGATIDAMTKLKPAFDKDGTVTA 243

Query: 243 ANASGLNDGAAATLLMSADDAEKRGIEPLARIASYATAGLDPSIMGVGPIYASRKALEKA 302
           ANASG+NDGAA  LLMS  +A +RGI PLARI S+ATAG+DP IMG GPI ASRKALEKA
Sbjct: 244 ANASGINDGAAGALLMSEAEAVRRGITPLARIVSWATAGVDPQIMGTGPIPASRKALEKA 303

Query: 303 GWSVDDLDLVEANEAFAAQACAVNKDMGWDPAIVNVNGGAIAIGHPIGASGCRVLNTLLF 362
           GWSV DLDLVEANEAFAAQACAVNKDMGWDP+IVNVNGGAIAIGHPIGASG RV NTL+F
Sbjct: 304 GWSVGDLDLVEANEAFAAQACAVNKDMGWDPSIVNVNGGAIAIGHPIGASGARVFNTLVF 363

Query: 363 EMKRRDAKKGLATLCIGGGMGVAMCVE 389
           EM+RR AKKGLATLCIGGGMGVAMCVE
Sbjct: 364 EMRRRGAKKGLATLCIGGGMGVAMCVE 390


Lambda     K      H
   0.316    0.130    0.376 

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: 522
Number of extensions: 8
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: 391
Length of database: 392
Length adjustment: 31
Effective length of query: 360
Effective length of database: 361
Effective search space:   129960
Effective search space used:   129960
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 YP_004140539.1 Mesci_1329 (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.26126.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   2.3e-145  470.3   9.4   2.6e-145  470.1   9.4    1.0  1  lcl|NCBI__GCF_000185905.1:YP_004140539.1  Mesci_1329 acetyl-CoA acetyltran


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000185905.1:YP_004140539.1  Mesci_1329 acetyl-CoA acetyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  470.1   9.4  2.6e-145  2.6e-145       1     385 []       7     390 ..       7     390 .. 0.98

  Alignments for each domain:
  == domain 1  score: 470.1 bits;  conditional E-value: 2.6e-145
                                 TIGR01930   1 ivdavRtpigklggslkelsaedLlaavikelleragldpekidevilGnvlqageqaniaReaalaag 69 
                                               i +a+Rtp+g+++g+++ ++a++L+a vi+ell rag++p ++devilG+vl+a++++n+aR+a ++ag
  lcl|NCBI__GCF_000185905.1:YP_004140539.1   7 IASAARTPVGSFNGAFAATPAHELGAVVIRELLSRAGVEPGEVDEVILGQVLTAAQGQNPARQASINAG 75 
                                               789****************************************************************** PP

                                 TIGR01930  70 lpesvpaltvnrvCaSglqAvalaaqkikaGeadvvvaGGvEsmSrvpillkaslrreslklgkakled 138
                                               lp+++ a+ +n+vC+Sgl+A+al++q+i+ G+a+v++aGG EsmS + +  +    r+++k+g++kl d
  lcl|NCBI__GCF_000185905.1:YP_004140539.1  76 LPKETTAWGLNQVCGSGLRAIALGMQQIAIGDARVIIAGGQESMSLSTHAQH---LRAGVKMGDFKLID 141
                                               *********************************************9975444...479*********** PP

                                 TIGR01930 139 qllkdl...vktklsmgetAenlakkygisReeqDeyalrShqkaakAieegkfkdeivpvevkgk..k 202
                                               +++kd+   + ++++mg+tAen+a++++i+Re+qD++al+S++ka++A+++gkfkdeiv v++kgk  +
  lcl|NCBI__GCF_000185905.1:YP_004140539.1 142 TMIKDGlwdAFNGYHMGNTAENVARQFQITREDQDQFALASQNKAEAAQKAGKFKDEIVAVTIKGKkgD 210
                                               *********99********************************************************99 PP

                                 TIGR01930 203 kvvskDegirpnttlekLakLkpafkekkgstvtAgNssqlnDGAaalllmseevakelgltplarivs 271
                                               ++v++De ir + t++++ kLkpaf++ +g tvtA+N+s++nDGAa +llmse+ a + g+tplarivs
  lcl|NCBI__GCF_000185905.1:YP_004140539.1 211 TIVDQDEYIRHGATIDAMTKLKPAFDK-DG-TVTAANASGINDGAAGALLMSEAEAVRRGITPLARIVS 277
                                               9************************95.9*.6************************************* PP

                                 TIGR01930 272 aavagvdpeemglgpvpAiekaLkkaglsisdidlvEinEAFAaqvlavekelgsldlekvNvnGGAiA 340
                                               +a+agvdp++mg+gp+pA++kaL+kag+s+ d+dlvE nEAFAaq+ av+k++g  d++ vNvnGGAiA
  lcl|NCBI__GCF_000185905.1:YP_004140539.1 278 WATAGVDPQIMGTGPIPASRKALEKAGWSVGDLDLVEANEAFAAQACAVNKDMG-WDPSIVNVNGGAIA 345
                                               ******************************************************.88************ PP

                                 TIGR01930 341 lGHPlGasGarivltllkeLkergkkyGlatlCvggGqGaAvile 385
                                               +GHP+GasGar+  tl+ e+++rg+k GlatlC+ggG+G+A+ +e
  lcl|NCBI__GCF_000185905.1:YP_004140539.1 346 IGHPIGASGARVFNTLVFEMRRRGAKKGLATLCIGGGMGVAMCVE 390
                                               ******************************************987 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (385 nodes)
Target sequences:                          1  (392 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: 8.37
//
[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