GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hcl in Kocuria flava HO-9041

Align Benzoate--CoA ligase; Benzoyl-CoA synthetase; EC 6.2.1.25 (characterized)
to candidate WP_058857116.1 AS188_RS00055 long-chain fatty acid--CoA ligase

Query= SwissProt::Q8GQN9
         (527 letters)



>NCBI__GCF_001482365.1:WP_058857116.1
          Length = 568

 Score =  179 bits (453), Expect = 3e-49
 Identities = 161/512 (31%), Positives = 227/512 (44%), Gaps = 47/512 (9%)

Query: 51  TYDELALRVNRCGSALRTTLGLQPKDRVLVCVLDGIDFPTTFLGAIKGGVVPIAINTLLT 110
           +Y  L  +V R    LR  LG+   DRV + + +       F   ++ G V +  N L T
Sbjct: 59  SYARLGEQVERAAEGLRR-LGVAAGDRVAIVLPNCPQHIVAFYAVLRLGAVVVEHNPLYT 117

Query: 111 ESDYEYMLTDSAARVAVVSQ----------ELLPLFAPMLGKVP------TLEHLVVAGG 154
             +  +   D  ARVA+V            E L L A +   V       T   L +   
Sbjct: 118 APELRHQFEDHGARVAIVWDRAADRIRSLPEDLRLDAVVAVDVTQAMPRRTRAALRLPLP 177

Query: 155 AGEDSLAALLA-----------TGSEQFEAAPTRPDDHCFWL--YSSGSTGAPKGTVHIH 201
           A   S A L               +E   A   RP  H   L  Y+SG+TG PKG +  H
Sbjct: 178 AARASRAQLTGPAPGTIPWRRLVAAEPLAADHPRPTAHDLALLQYTSGTTGLPKGAMLTH 237

Query: 202 SDLIHTAELYARPILGIREGDVVFSAAKLFFAYGLGNGLIFPLAVGATAVLMAERPTPAA 261
            +L   A L  +  L   E +VV     LF A+GL  G+ F +++GA  VL    PT  A
Sbjct: 238 RNLESNA-LMGQHWLHSGEDEVVHGVLPLFHAFGLTLGVTFAMSLGARLVLF---PTVRA 293

Query: 262 --VFERLRRHQPDIFYGVPTLYASMLANPDCPKEGELRLRA---CTSAGEALPEDVGRRW 316
             V + LRR +P +   VP +Y  +L   D  +E    LR      S    LP  +  RW
Sbjct: 294 DLVLKALRRSRPTVLPAVPPVYEKLL---DAAEERGADLRGIAVAVSGAMTLPVPLVERW 350

Query: 317 QARFGVDILDGIGSTEMLHIFLSNRAGDVHY-GTSGKPVPGYRLRLIDEDGAEITTAGVA 375
           +   G  +++G G TE   +   N   D    G+ G P P   +RL+D +  E    G  
Sbjct: 351 ERATGGMLVEGYGLTECSPLVACNPLNDSRRAGSIGVPFPSTEIRLVDPETLEDVPRGHE 410

Query: 376 GELQISGPSSAVMYWNNPEKTAATFMGE-WTRSGDKYLVNDEGYYVYAGRSDDMLKVSGI 434
           GEL + GP     YW  PE+TA   + + W R+GD   V+D+G+     R  +++   G 
Sbjct: 411 GELWVRGPQVFRGYWKRPEETARVLVEDGWLRTGDVVTVDDDGFLRVVDRIKEVIITGGF 470

Query: 435 YVSPIEVESALIAHEAVLEAAVVGWEDEDHLIKPKAFIVLKPGYGAGEALRTDLKAHVKN 494
            V+P EVE+AL  H+ V +AAVVG +D        A +VL PG    E     L+ H   
Sbjct: 471 NVAPTEVETALKLHDDVADAAVVGLDDGRGGEAVVAAVVLAPGAVLDEQA---LREHCYG 527

Query: 495 LLAPYKYPRWIEFVDDLPKTATGKIQRFKLRS 526
            +  YK PR I  V+DLP+T  GK  R ++R+
Sbjct: 528 KVTRYKVPRRIVAVEDLPRTMLGKTLRREVRA 559


Lambda     K      H
   0.319    0.138    0.412 

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: 56
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 527
Length of database: 568
Length adjustment: 36
Effective length of query: 491
Effective length of database: 532
Effective search space:   261212
Effective search space used:   261212
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 (21.7 bits)
S2: 53 (25.0 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