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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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:

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:

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:

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:

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