GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ1 in Flavobacterium glycines Gm-149

Align 3-ketoacyl-CoA thiolase, peroxisomal; Acetyl-CoA acyltransferase; Beta-ketothiolase; Peroxisomal 3-oxoacyl-CoA thiolase; EC 2.3.1.16 (characterized)
to candidate WP_066324593.1 BLR17_RS15680 acetyl-CoA C-acyltransferase

Query= SwissProt::P09110
         (424 letters)



>NCBI__GCF_900100165.1:WP_066324593.1
          Length = 393

 Score =  300 bits (767), Expect = 7e-86
 Identities = 172/387 (44%), Positives = 239/387 (61%), Gaps = 7/387 (1%)

Query: 40  VVHGRRTAICRAGRGGFKDTTPDELLSAVMTAVLKDV-NLRPEQLGDICVGNVL-QPGAG 97
           +V   RTA+ +A +G F+   PDEL +  +  ++ ++ +   +++ D+ VGN + +   G
Sbjct: 6   IVKAYRTAVGKAPKGLFRFKRPDELAAETIQHMMNELPDFDKKRIDDVMVGNAMPEAEQG 65

Query: 98  AIMARIAQFLSDIPETVPLSTVNRQCSSGLQAVASIAGGIRNGSYDIGMACGVESMSLAD 157
               R+   +      VP  TVNR C+SGL+ +      I++G  D  +A G ESMS   
Sbjct: 66  LNFGRLISLMGLEINDVPGVTVNRYCASGLETIGMATARIQSGMADCIIAGGAESMSFIP 125

Query: 158 RGNPGNITSRLMEKEKARDCLIPMGITSENVAERFGISREKQDTFALASQQKAARAQSKG 217
            G         + K    D    MG+T+E VA++F ISRE QD FA  S QKA +AQ++G
Sbjct: 126 MGGYKPTPDYALAKAGHEDYYWGMGLTAEAVAKQFNISREDQDLFAYNSHQKALKAQAEG 185

Query: 218 CFQAEIVPVTT--TVHDDKGTKR--SITVTQDEGIRPSTTMEGLAKLKPAFKKDGSTTAG 273
            F ++IVP+T   T  + KG K   S TV +DEG R  T++E LAKL+P F  DGS TAG
Sbjct: 186 KFDSQIVPITVEQTFINAKGKKETTSYTVNKDEGPRADTSLEALAKLRPVFAADGSVTAG 245

Query: 274 NSSQVSDGAAAILLARRSKAEELGLPILGVLRSYAVVGVPPDIMGIGPAYAIPVALQKAG 333
            SSQ+SDGAA +L+      +EL L  +  L +YA  GV P IMGIGP  AIP AL++AG
Sbjct: 246 TSSQMSDGAAFVLIMSEELVKELNLTPIARLVNYASAGVEPRIMGIGPVKAIPKALKQAG 305

Query: 334 LTVSDVDIFEINEAFASQAAYCVEKLRLPPEKVNPLGGAVALGHPLGCTGARQVITLLNE 393
           L + D+D+ E+NEAFASQ+   + +L L P+ VN  GGA+ALGHPLGCTGA+  + L NE
Sbjct: 306 LQLKDIDLIELNEAFASQSLAVIRELGLNPDIVNVNGGAIALGHPLGCTGAKLSVQLFNE 365

Query: 394 LKRRGKRAYGVVSMCIGTGMGAAAVFE 420
           +KRRG + YG+V+MC+GTG GAA +FE
Sbjct: 366 MKRRGNK-YGMVTMCVGTGQGAAGIFE 391


Lambda     K      H
   0.317    0.134    0.385 

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: 414
Number of extensions: 16
Number of successful extensions: 4
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: 424
Length of database: 393
Length adjustment: 31
Effective length of query: 393
Effective length of database: 362
Effective search space:   142266
Effective search space used:   142266
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: 50 (23.9 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