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_004140285.1 Mesci_1071 3-hydroxyacyl-CoA dehydrogenase NAD-binding protein

Query= BRENDA::Q64428
         (763 letters)



>NCBI__GCF_000185905.1:YP_004140285.1
          Length = 688

 Score =  326 bits (835), Expect = 3e-93
 Identities = 226/716 (31%), Positives = 357/716 (49%), Gaps = 47/716 (6%)

Query: 47  GDVAVIRINSPNSKVNTLNKEVQSEFVEVMNEIWANDQIRSAVLISSKPGCFVAGADINM 106
           GDVAV+ I++P   VN L+  V+   ++ + E+  +D   +A++I+     FVAGADI  
Sbjct: 11  GDVAVVTIDNP--PVNALSFHVREPLMQALVEL-RDDASVAAIVIACAGRTFVAGADITE 67

Query: 107 LASCTTPQEAARISQEGQKMFEKLEKSPKPVVAAISGSCLGGGLELAIACQYRIATKDRK 166
                   E   I          LE   KP VAAI G+ LGGGLELA+ C +R+A    K
Sbjct: 68  FGKPMQQPELRAI-------VATLETIAKPTVAAIHGTALGGGLELALGCHFRVADAGAK 120

Query: 167 TVLGVPEVLLGILPGAGGTQRLPKMVGVPAAFDMMLTGRNIRADRAKKMGLVDQLVDPLG 226
             LG+PEV LG+LPG GGT RLP++VG   A  M+++G  I A  A   GLVD + +   
Sbjct: 121 --LGLPEVKLGLLPGGGGTVRLPRLVGAVKALKMIVSGAPIGATEAHAAGLVDAVFEG-- 176

Query: 227 PGIKSPEERTIEYLEEVAVNFAKGLADRKVSAKQSKGLMEKLTSYAMTIPFVRQQVYKTV 286
                        L   AVNFA  +A +       +   E L    +         +   
Sbjct: 177 ------------DLTTHAVNFAGEIARKGGPFTPVRDRNEGLKQADLA-------AFDVE 217

Query: 287 EEKVKKQTKGLYPAPLKIIDAVKTGLEQGNDAGYLAESEKFGELALTKESKALMGLYNGQ 346
              + ++ +GL  AP+    +V+  +    DA   AE   F +L  + +S+A   L+  +
Sbjct: 218 AADLARKARGL-EAPIACAQSVRNAVTLPFDAALAAERALFVKLVASDQSRAQRHLFFAE 276

Query: 347 -VLCKKNKFGAPQKTVQQLAILGAGLMGAGIAQVSVDKGLKTLLKDTTVTGLGRGQQQVF 405
               K       ++ + ++ ++GAG MG GIA    + G   +L +T+   L RG   + 
Sbjct: 277 REAAKLPGKDIVKRRIARVGVIGAGTMGGGIAMAFANGGYSVILLETSHEALQRGLATID 336

Query: 406 KGLNDKVKKKALTSFERDSIFSNLIGQLDYKGFEKADMVIEAVFEDLAVKHKVLKEVESV 465
           +  +  V + +L+   +    +   G  DY      D+++EAVFED+AVK +V  ++E+V
Sbjct: 337 RNYSVSVTRGSLSEDAKRQRLAQFKGSTDYVDLADCDLIVEAVFEDMAVKKEVFGKLEAV 396

Query: 466 TPEHCIFASNTSALPINQIAAVSQRPEKVIGMHYFSPVDKMQLLEIITTDKTSKDTTASA 525
                I A+NTS L IN+IA  + RP+ V+G+H+FSP + M+LLEI+  +KT+ D  A++
Sbjct: 397 AKPGAILATNTSYLDINEIAGSTSRPQDVLGLHFFSPANVMKLLEIVRAEKTAPDALATS 456

Query: 526 VAVGLKQGKVIIVVKDGPGFYTTRCLAPMMSEVIRILQEGVDPKKLDALTTGFGFPVGAA 585
           V +  + GKV +VV    GF   R LA   SE   +L EG  P ++D + T FG+P+G  
Sbjct: 457 VDLARRIGKVAVVVGVCHGFVGNRMLAARGSESEALLLEGATPSQIDQVFTDFGWPMGPF 516

Query: 586 TLADEVGIDVAQHVAEDLGKAFGERFGGGSVELLKLMVSKGFLGRKSGKGFYIYQSGSKN 645
            + D  G+D+              +  G    +   +  +G  G+K+G+GFY+Y++G++ 
Sbjct: 517 QMGDLAGLDIGWR---------NRKARGQKAVIADTLCEQGRFGQKTGRGFYLYEAGART 567

Query: 646 KNLNSEIDNILVNLRLP--AKPEVSSDEDIQYRVITRFVNEAVLCLQEGILATPEEGDIG 703
              + E++ ++ +        P   S E+I  R +   +NE    L+EGI A   + D+ 
Sbjct: 568 PVPDPEVEALIRDKAAENGIAPRAISAEEIVERTLYPLINEGAKILEEGIAARASDIDVV 627

Query: 704 AVFGLGFPPCLGGPFRFVDLYGAQKVVDRLRKYESAYGTQ-FTPCQLLRDLANNSS 758
            V G GFP   GGP  +V L G  ++++RL  +    G   F P  LL+ +A   S
Sbjct: 628 WVNGYGFPIGKGGPMFWVGLEGPARIIERLEYWHQRTGKDVFKPAPLLKRMAETGS 683


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: 1059
Number of extensions: 53
Number of successful extensions: 7
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: 763
Length of database: 688
Length adjustment: 40
Effective length of query: 723
Effective length of database: 648
Effective search space:   468504
Effective search space used:   468504
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:

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