GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ1 in Pedobacter sp. GW460-11-11-14-LB5

Align Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) (characterized)
to candidate CA265_RS17585 CA265_RS17585 acetyl-CoA acetyltransferase

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



>FitnessBrowser__Pedo557:CA265_RS17585
          Length = 391

 Score =  289 bits (739), Expect = 1e-82
 Identities = 181/412 (43%), Positives = 237/412 (57%), Gaps = 35/412 (8%)

Query: 9   DAYIVDAIRTPIGRYG-GALSAVRADDLGAIPIKALAERYPDLDWSKIDDVLYGCANQAG 67
           +AYI+   RT +G+   G     RADDL A  I+AL    P+LD  +IDDV+ G A    
Sbjct: 2   EAYIIAGYRTAVGKAPRGVFRFTRADDLAAEVIRALVASVPNLDNEQIDDVIVGNATPEA 61

Query: 68  EDNRDVARMSLLLAGLPVD-VPGSTINRLCGSGMDAVGSAARAIRTGETQLMIAGGVESM 126
           E   ++ RM + L GL  D VPG T+NR C SG+D + +A   I+ G    +IAGGVE M
Sbjct: 62  EQGLNIGRM-ISLMGLDTDKVPGVTVNRYCASGLDTIATAVAKIKAGMADCIIAGGVEVM 120

Query: 127 SRAPFVMGKADSAFSRKAEIFDTTIGWRFVNPVLKKQYGIDSMPETAENVAADFGISRED 186
           S  PF   K        AE+      W +             M  TAE VA ++ +SRED
Sbjct: 121 SGMPFGGWK----LVPNAEVAKNNPDWYW------------GMGLTAEAVAKEYNVSRED 164

Query: 187 QDAFALRSQQRTAAAQKEGRLAAEITPVTIP--------RRKQDPLVVDTDEHPR-ETSL 237
           QDAF+L+S ++   A K G L   I P+T+         ++K    VVDTDE PR +T+L
Sbjct: 165 QDAFSLKSHEKAIHAIKNGHLKDGILPITVNENYLDANLKKKTRSYVVDTDEGPRADTTL 224

Query: 238 EKLASLPTPFRENGTVTAGNASGVNDGACALLLAGADALKQYNLKPRARVVAMATAGVEP 297
           +KLA L   F   G+VTAGN+S  +DGA  +L+     +K+ N +P AR+V+   AGV P
Sbjct: 225 DKLAKLKPVFDAVGSVTAGNSSQTSDGAAFVLVVSEKKMKELNAEPIARLVSYGIAGVPP 284

Query: 298 RIMGFGPAPATRKVLATAGLELADMDVIELNEAFAAQALAVTRDLGLPDDAEHVNPNGGA 357
           RIMG GP  A  K L  AGL+  D+D+IELNEAFA+Q+LAV R L L  D   +N NGGA
Sbjct: 285 RIMGIGPIEAIPKALKQAGLKKEDIDLIELNEAFASQSLAVIRTLDLNPDV--INVNGGA 342

Query: 358 IALGHPLGMSGARLVTTALNELERRHAAGQKARYALCTMCIGVGQGIALIIE 409
           IALGHPLG +GA+L    +NEL+R     Q  +Y + TMC+G GQG A I E
Sbjct: 343 IALGHPLGCTGAKLTVQIMNELKR-----QNKKYGMVTMCVGTGQGAAGIFE 389


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: 427
Number of extensions: 20
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: 415
Length of database: 391
Length adjustment: 31
Effective length of query: 384
Effective length of database: 360
Effective search space:   138240
Effective search space used:   138240
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 17 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