GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuD in Algoriphagus aquaeductus T4

Align Methylcrotonoyl-CoA carboxylase (EC 6.4.1.4) (characterized)
to candidate WP_111394452.1 CLV31_RS17930 acyl-CoA carboxylase subunit beta

Query= reanno::SB2B:6937191
         (535 letters)



>NCBI__GCF_003253485.1:WP_111394452.1
          Length = 538

 Score =  487 bits (1254), Expect = e-142
 Identities = 250/521 (47%), Positives = 343/521 (65%), Gaps = 17/521 (3%)

Query: 28  DLKDKLAHIEQGGGLVAMERHLSRGKLAPRARVEKLLDPGSPFLELSQFAAFEVYDED-- 85
           +L+ K+  ++ GGG   +     +GKL  R R++ L+D  S FLE+  FAA  +Y E+  
Sbjct: 14  ELRSKMTQVKLGGGPKRIAAEHEKGKLTARERIDYLIDEDSEFLEIGIFAADGMYQEEGG 73

Query: 86  VPAAGIIAGIGRVSGVECMIIANDATVKGGTYYPITVKKHLRAQAIAERCHLPCIYLVDS 145
            P+AG++ GIG VSG  C+I+ANDATVK G ++P+T KK+LRAQ IA    LP IYLVDS
Sbjct: 74  CPSAGVVTGIGMVSGRMCVIVANDATVKAGAWFPMTAKKNLRAQEIAMENRLPIIYLVDS 133

Query: 146 GGANLPRQDEVFPDRDHFGRIFFNQARMSAKGIPQIAVVMGLCTAGGAYVPAMADESIIV 205
            G  LP Q+E+FPD++HFGR F N A+MSA GI Q+A +MG C AGGAY+P M+DE++IV
Sbjct: 134 AGVFLPMQNEIFPDKEHFGRQFRNNAKMSAMGIVQVAAIMGSCVAGGAYLPIMSDEALIV 193

Query: 206 REQGTIFLAGPPLVKAATGEEVSAEELGGGDVHTKISGVADHLAQNDEHALELARKAVSR 265
            + G+IFLAG  LV+AA GE V  E LGG   H +ISGV D+   ND+  L+  R+    
Sbjct: 194 DKTGSIFLAGSYLVRAAIGENVDNETLGGATTHCEISGVTDNKYANDQECLDAIRRIFET 253

Query: 266 LNHQKQVELQLSKVKPPKYDINELYGIVGTDLKKPFDVKEVIARIVDDSDFDEFKANYGT 325
           L  Q +        K P     +L  I   D  KP+D+ +V+  ++D+   +E+K +YG 
Sbjct: 254 LGDQPKAGFDRIGTKQPSLSQEKLLEIFPIDRAKPYDMHQVLEGLIDEGSLEEYKKDYGK 313

Query: 326 TLVCGFARIHGYPVGIVAN--------------NGILFSESAQKGAHFIELCCQRKIPLV 371
           TL+CG ARI G+ VGIVAN               G+++S+SA K A FI  C QRKIPLV
Sbjct: 314 TLICGTARIDGWAVGIVANQRKIVKTAKGEMQMGGVIYSDSADKAARFIMNCNQRKIPLV 373

Query: 372 FLQNITGFMVGKKYEHEGIAKHGAKMVTAVSCATVPKFTVLIGGSYGAGNYGMCGRAFEP 431
           FLQ+++GFMVG K EH GI K GAKMV A++ + VPKFT+++G SYGAGNY MCG+A++P
Sbjct: 374 FLQDVSGFMVGSKAEHGGIIKDGAKMVNAMANSVVPKFTLVVGNSYGAGNYAMCGKAYDP 433

Query: 432 TLMWMWPNARISVMGGEQAAGVLATVRKDGLARKGETMSAEEEAKFKAPIIAQYDKEGHP 491
            L++ WP A+++VM G  AA  L  ++   L + G+ +S EEE +    I+A+Y++E  P
Sbjct: 434 RLIFSWPTAQMAVMSGASAAKTLLQIKVASLKKSGKEISPEEEKQLLDEIVAKYNEELSP 493

Query: 492 YHASARLWDDGIIDPAQTRDVLGLAISAALNAPIEETRFGV 532
           Y+A+ARLW DG+IDP +TR V+   I+AA +API E RF V
Sbjct: 494 YYAAARLWVDGVIDPRETRKVISAGIAAANHAPITE-RFNV 533


Lambda     K      H
   0.320    0.137    0.405 

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: 795
Number of extensions: 37
Number of successful extensions: 3
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: 535
Length of database: 538
Length adjustment: 35
Effective length of query: 500
Effective length of database: 503
Effective search space:   251500
Effective search space used:   251500
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 52 (24.6 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