GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadA in Methylocystis bryophila S285

Align long-chain-3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.211); acetyl-CoA C-acyltransferase (EC 2.3.1.16) (characterized)
to candidate WP_085772004.1 B1812_RS13170 3-hydroxyacyl-CoA dehydrogenase NAD-binding domain-containing protein

Query= BRENDA::Q64428
         (763 letters)



>NCBI__GCF_002117405.1:WP_085772004.1
          Length = 728

 Score =  335 bits (860), Expect = 4e-96
 Identities = 235/757 (31%), Positives = 370/757 (48%), Gaps = 62/757 (8%)

Query: 36  LSRTHINYGVKGDVAVIRINSPNSKVNTLNKEVQSEFVEVMNEIWANDQIRSAVLISSKP 95
           L     + G  G VA++  + P   +N + +EV SE  +V+ ++ A+  I+  V+ S K 
Sbjct: 3   LQNFRFDVGADG-VALLTWDMPGRSMNVITEEVMSELAQVVEKVAADAAIKGCVIASGK- 60

Query: 96  GCFVAGADINMLASCTTP----------QEAARISQEGQK----MFEKLEKSPKPVVAAI 141
             F  GAD++ML                +EA R+  E  +    ++ +LE   KP   AI
Sbjct: 61  NAFSGGADLSMLQKSRAAHGKALGEKGAEEANRLFFESARKLSQLYRRLETCGKPFAIAI 120

Query: 142 SGSCLGGGLELAIACQYRIATKDRKTVLGVPEVLLGILPGAGGTQRLPKMVGVPAAFDMM 201
            G CLGG  ELA+AC +R+   D KT +G+PEV +G+ PGAGGTQR+ +++    A   +
Sbjct: 121 HGVCLGGAFELALACHHRVLADDDKTKVGLPEVKVGLFPGAGGTQRVARIMPTGDALQFL 180

Query: 202 LTGRNIRADRAKKMGLVDQLVDPLGPGIKSPEERTIEYLEEVAVNFAKGLA--DRKVSAK 259
             G  +    AK  GL  +L         +P+   +   ++  +   K +A  D+K   K
Sbjct: 181 FKGEQLSGKAAKAAGLAQEL---------APQSEIVSRAKDWILGGGKAIAPWDQK-DFK 230

Query: 260 QSKGLMEKLTSYAMTIPFVRQQVYKTVEEKVKKQTKGLYPAPLKIIDAVKTGLEQGNDAG 319
              G +   +   M I      +Y+       ++T   YPA   I+  V  GL+   D G
Sbjct: 231 PPSGRI--FSPGGMMIWMPANAIYR-------RETYDNYPAVKAILHCVYEGLQLPIDQG 281

Query: 320 YLAESEKFGELALTKESKALMGLYNGQVLCKKNKF--GA------PQKTVQQLAILGAGL 371
              E+  F  +  +KE+ A++      +   KN+   GA      P   ++++ +LGAG 
Sbjct: 282 LTVEARWFAHILRSKEAAAMIR----SLFLSKNELDKGARRPKDEPPTQLKKIGVLGAGF 337

Query: 372 MGAGIAQVSVDKGLKTLLKDTTVTGLGRGQQQVFKGLNDKVKKKALTSFERDSIFSNLIG 431
           MGAG+  VS   GL+ +L D       +G+  + K ++ +V +   T+  ++++ + +  
Sbjct: 338 MGAGVGYVSALNGLEVVLIDRDQESADKGKATIDKLISGQVSRGKATASAKEALLARVEA 397

Query: 432 QLDYKGFEKADMVIEAVFEDLAVKHKVLKEVESVTPEHCIFASNTSALPINQIAAVSQRP 491
             DY+  +  D+++EAVFED AVK +  K  ++      +FASNTS LPI  +A  S +P
Sbjct: 398 TPDYERLKGCDLILEAVFEDRAVKAEATKRAQAAVGPDVVFASNTSTLPITSLAETSLKP 457

Query: 492 EKVIGMHYFSPVDKMQLLEIITTDKTSKDTTASAVAVGLKQGKVIIVVKDGPGFYTTRCL 551
           E  IG+H+FSPV+KM L+EII  +KTS    A+A+       K  IVV D  GF+  RC+
Sbjct: 458 ENFIGVHFFSPVEKMLLVEIILGEKTSDKALATALDFVRMIKKTPIVVNDSRGFFANRCV 517

Query: 552 APMMSEVIRILQEGVDPKKLDALTTGFGFPVGAATLADEVGID----VAQHVAEDLGKAF 607
              + E   +L EGV P  ++      G PVG  +L DEVG+D    + Q   +DLG A 
Sbjct: 518 LAYVREGQTMLVEGVPPAMIENAARMAGMPVGPLSLNDEVGLDLGWKILQATKKDLGAA- 576

Query: 608 GERFGGGSVELLKLMVSK-GFLGRKSGKGFYIYQSGSKNKNLNSEIDNILVNLRLPAKPE 666
                     +L  +V K G  GRK+GKGFY Y +  K K L   +  +         P+
Sbjct: 577 --AVDPAQERVLGFLVEKNGRFGRKNGKGFYDYPASGK-KTLWPGLAGL---AEKTLDPD 630

Query: 667 VSSDEDIQYRVITRFVNEAVLCLQEGILATPEEGDIGAVFGLGFPPCLGGPFRFVDLYGA 726
               ++++ R +     EA     E ++  P E D+G++ G GF P  GG   ++D  G 
Sbjct: 631 AIDVKELERRFLVAQAVEAARTFAEHVVTDPREADVGSILGFGFAPFTGGALSYIDGMGL 690

Query: 727 QKVVDRLRKYESAYGTQFTPCQLLRDLANNSSKKFYQ 763
           +  V       + YG +F P QLLRD+A    + FY+
Sbjct: 691 KAFVALCDTLAAKYGPRFAPPQLLRDMA-REGETFYR 726


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: 1144
Number of extensions: 54
Number of successful extensions: 6
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: 728
Length adjustment: 40
Effective length of query: 723
Effective length of database: 688
Effective search space:   497424
Effective search space used:   497424
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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