GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ1 in Pseudovibrio axinellae Ad2

Align Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) (characterized)
to candidate WP_068004809.1 PsAD2_RS08250 thiolase family protein

Query= reanno::Marino:GFF2751
         (415 letters)



>NCBI__GCF_001623255.1:WP_068004809.1
          Length = 383

 Score =  157 bits (397), Expect = 5e-43
 Identities = 134/418 (32%), Positives = 199/418 (47%), Gaps = 56/418 (13%)

Query: 11  YIVDAIRTPIGRYG--GALSAVRADDLGAIPIKALAERYPDLDWSKIDDVLYGCANQAGE 68
           YI DA+RT  G+    G L+AV+ D+L A    A+ +R       K + +L G   Q G 
Sbjct: 4   YIYDAVRTARGKAKPEGGLAAVKPDELVAALSDAITDRVGQF---KPEALLLGSVGQVGA 60

Query: 69  DNRDVARMSLLLAGLPVDVPGSTINRLCGSGMDAVGSAARAIRTGETQLMIAGGVESMSR 128
              ++A +S   A LP +    TIN  C SG+ A+G A+  + TG+   ++AGGVE MS 
Sbjct: 61  QGGNIALVSKFRAKLPDETVAWTINNFCASGLTAIGQASSMVATGQANRVLAGGVEMMSC 120

Query: 129 APFVMGKADSAFSRKAEIFDTTIGWRFVNPVLKKQYGIDSMPETAENVAADFGISREDQD 188
            PF+   AD A               +V+  L +++    +   A+ +A D  ISR + D
Sbjct: 121 VPFM---ADDAH-------------YYVDTTLPERHRYLLVALAADKLAEDLDISRAEMD 164

Query: 189 AFALRSQQRTAAAQKEGRLAAEITPVTIPRRKQDPLVVDTDEHPRETSLEKLASLPTPF- 247
             ALRS  +       G+ A+ I    + R          +E  ++   E +A+L   F 
Sbjct: 165 TAALRSHAQALLGDDNGKNASRIIVNGLNR----------EECAKKMDHESIAALQPAFA 214

Query: 248 ------------RENGTVTAGNASGVNDGACALLLAGADALKQYNLKPRARVVAMATAGV 295
                       + +   T  +A  + DGA   ++    A+   +  PRA++VA A  G 
Sbjct: 215 ALAPQYAQVLGRKVDHRHTIAHAPPMTDGAGLAMVGTYGAI---DAPPRAQIVAFAEVGG 271

Query: 296 EPRI-MGFGPAPATRKVLATAGLELADMDVIELNEAFAAQALAVTRDLGLPDDAEHVNPN 354
           +P + +G G A A  +VLA + L L DMD IE  EAFA   +   RD   P   + VN +
Sbjct: 272 DPAVSLGAGFA-AMDQVLAKSELSLEDMDRIEFMEAFAVTIVKFLRD--HPHLEDRVNTS 328

Query: 355 GGAIALGHPLGMSGARLVTTALNELERRHAAGQKARYALCTMCIGVGQGIALIIERMD 412
           GG +A GHPLG SGA LV+T L+ L+       + RY L       G G A+I++RMD
Sbjct: 329 GGHLAKGHPLGASGAILVSTLLDTLDM-----VQGRYGLVVASGAEGIGSAMIVKRMD 381


Lambda     K      H
   0.318    0.133    0.382 

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: 364
Number of extensions: 19
Number of successful extensions: 5
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: 415
Length of database: 383
Length adjustment: 31
Effective length of query: 384
Effective length of database: 352
Effective search space:   135168
Effective search space used:   135168
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