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 long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211); acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate YP_004145058.1 Mesci_6001 3-hydroxyacyl-CoA dehydrogenase NAD-binding protein

Query= BRENDA::Q64428
         (763 letters)



>NCBI__GCF_000185905.1:YP_004145058.1
          Length = 739

 Score =  364 bits (934), Expect = e-104
 Identities = 242/750 (32%), Positives = 374/750 (49%), Gaps = 51/750 (6%)

Query: 39  THINYGVKGD---VAVIRINSPNSKVNTLNKEVQSEFVEVMNEIWANDQIRSAVLISSKP 95
           ++ N+ +  D   +A++  + P   +N   +E   E   +++++  +  I+ AV+ S K 
Sbjct: 2   SYTNFALDTDADGIALVTWDMPGRSMNVFTEEAMRELNAIVDKVAGDAAIKGAVITSGKD 61

Query: 96  GCFVAGADINMLASCTTPQEAARISQEGQK--------------MFEKLEKSPKPVVAAI 141
             F  GADI++L    T   AA   ++ +K              +F KLE   KP V+AI
Sbjct: 62  -TFSGGADISLLQKMLTTF-AAEKGKDAEKATKALFDNAGMMTGLFRKLETCGKPWVSAI 119

Query: 142 SGSCLGGGLELAIACQYRIATKDRKTVLGVPEVLLGILPGAGGTQRLPKMVGVPAAFDMM 201
           +G+C+GG  EL++AC  R+A    K  + +PEV +GI PGAGGTQR+P++     A  M+
Sbjct: 120 NGTCMGGAFELSLACHGRVAADSDKVKMALPEVKIGIFPGAGGTQRVPRLTDQQQALQML 179

Query: 202 LTGRNIRADRAKKMGLVDQLVDPLGPGIKSPEERTIEYLEEVAVNFAKGLA--DRKVSAK 259
            +G+ +   +AK MGL+ ++ +P          R +E  + +  N  K +A  D K   K
Sbjct: 180 TSGQTLSPQKAKSMGLIHEIAEP---------TRLVETAKAMIRNGLKPVAPWDEK-GFK 229

Query: 260 QSKGLMEKLTSYAMTIPFVRQQVYKTVEEKVKKQTKGLYPAPLKIIDAVKTGLEQGNDAG 319
              G +     + +  P +           ++++T G YPA   I+  V  GL    D  
Sbjct: 230 LPGGQIYSPAGFNLWPPAI---------AILRRETYGNYPAAAAILKCVYEGLLVPFDTA 280

Query: 320 YLAESEKFGELALTKESKALMG--LYNGQVLCK--KNKFGAPQKTVQQLAILGAGLMGAG 375
              E   F E+  T+E+ A++     + Q L K  +   G P+   +++ ILGAG MGAG
Sbjct: 281 LRIEQRYFTEIMQTREAAAMIRSLFVSLQELNKGARRPAGVPETKFKKIGILGAGFMGAG 340

Query: 376 IAQVSVDKGLKTLLKDTTVTGLGRGQQQVFKGLNDKVKKKALTSFERDSIFSNLIGQLDY 435
           IA V+   G+  +L D  +    +G+      ++D+VKK      ++D + S +    DY
Sbjct: 341 IAYVTAKAGIPVVLLDRDLESAAKGKAHSDSLVSDQVKKGRAKPEDKDKLLSLITPTADY 400

Query: 436 KGFEKADMVIEAVFEDLAVKHKVLKEVESVTPEHCIFASNTSALPINQIAAVSQRPEKVI 495
                 D+V+EAVFED  VK    ++ E+V     IFASNTS +PI+ +A  S RP+  I
Sbjct: 401 ADLAGCDLVVEAVFEDSGVKKSATEQAEAVLKPSAIFASNTSTIPISSLAKNSARPKNFI 460

Query: 496 GMHYFSPVDKMQLLEIITTDKTSKDTTASAVAVGLKQGKVIIVVKDGPGFYTTRCLAPMM 555
           G+H+FSPVDKM L+EII   KT     A+A+       K  IVV D  GFY  RC+   M
Sbjct: 461 GIHFFSPVDKMMLVEIILGKKTGDKALATAIDFVRAIKKTPIVVNDTRGFYVNRCVLRYM 520

Query: 556 SEVIRILQEGVDPKKLDALTTGFGFPVGAATLADEVGIDVAQHVAEDLGKAFGER-FGGG 614
           SE  ++L EGV    ++      G PVG   L DE  ID+AQ + +   +  G++     
Sbjct: 521 SEAYKMLIEGVPAPMIENAAKAAGMPVGPLALTDETAIDLAQKIMKQTIRDLGDKAVDPK 580

Query: 615 SVELLKLMV-SKGFLGRKSGKGFYIYQSGSKNKNLNSEIDNILVNLRLPAKPEVSSDEDI 673
            + L+  MV   G  GRK+GKGFY Y +    K L   +  +   L     PE    E++
Sbjct: 581 QMALINTMVDDHGRFGRKNGKGFYDYPAKPAKKKLWPGLKELYPQL----APEKVDYEEL 636

Query: 674 QYRVITRFVNEAVLCLQEGILATPEEGDIGAVFGLGFPPCLGGPFRFVDLYGAQKVVDRL 733
           Q R++     EA   ++EGI+  P E D+G++   GF P  GG   ++D  GA+  V   
Sbjct: 637 QQRLLVTIALEAARVMEEGIVTDPREADVGSILAFGFAPYTGGALSYIDGIGAKAFVKIA 696

Query: 734 RKYESAYGTQFTPCQLLRDLANNSSKKFYQ 763
           R  +  YG +F   +LL D+A    + FYQ
Sbjct: 697 RNLQKKYGAEFKAPKLLLDMA-EKGESFYQ 725


Lambda     K      H
   0.317    0.135    0.380 

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: 1173
Number of extensions: 51
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 763
Length of database: 739
Length adjustment: 40
Effective length of query: 723
Effective length of database: 699
Effective search space:   505377
Effective search space used:   505377
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: 55 (25.8 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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