GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ1 in Chromobacterium vaccinii MWU205

Align Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) (characterized)
to candidate WP_046156966.1 VL52_RS10355 acetyl-CoA C-acyltransferase

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



>NCBI__GCF_000971335.1:WP_046156966.1
          Length = 400

 Score =  291 bits (744), Expect = 3e-83
 Identities = 192/415 (46%), Positives = 242/415 (58%), Gaps = 33/415 (7%)

Query: 7   LKDAYIVDAIRTPIGRYG-GALSAVRADDLGAIPIKALAERYPDLDWSKIDDVLYGCANQ 65
           +++AYIV A RTP+G+   G +  VR DD+ A  I     + P+LD   I D + GCA  
Sbjct: 5   VQEAYIVAATRTPVGKAPRGMMRNVRPDDMLAHVITGALAQVPNLDPKLISDCVVGCAFP 64

Query: 66  AGEDNRDVARMSLLLAGLPVDVPGSTINRLCGSGMDAVGSAARAIRTGETQLMIAGGVES 125
             E   ++AR+ +LLAGLP  V G TINR C SG++AV  AA  IR GE  ++IA G ES
Sbjct: 65  EAEQGLNMARIGVLLAGLPNTVGGITINRYCSSGINAVQMAADRIRLGEADVVIAAGSES 124

Query: 126 MSRAPFVMGKADSAFSRKAEIFDTTIGWRFVNPVLKKQYGID-SMPETAENVAADFGISR 184
           MS  P +  K     S   +IF              + YGI   M  TAE VA  +G+SR
Sbjct: 125 MSLVPMMGNKV----SLNPQIF-----------AKDENYGIAYGMGLTAEKVAQQWGVSR 169

Query: 185 EDQDAFALRSQQRTAAAQKEGRLAAEITPVTIPRRKQD---------PLVVDTDEHPR-E 234
           EDQDAFA+ S +R  AA   G+  +EITP+ +  R  +           V+DTDE PR E
Sbjct: 170 EDQDAFAVESHRRALAAIDGGKFKSEITPLEVTYRTPNLETGEVIAKTRVLDTDEGPRRE 229

Query: 235 TSLEKLASLPTPFRENGTVTAGNASGVNDGACALLLAGADALKQYNLKPRARVVAMATAG 294
           T+LE LA L T F   G+VTAGN+S ++DGA A++L     LK++NL P AR V  +  G
Sbjct: 230 TTLEGLAKLKTVFDAKGSVTAGNSSQMSDGAGAVILVSERVLKEFNLVPLARYVTFSVKG 289

Query: 295 VEPRIMGFGPAPATRKVLATAGLELADMDVIELNEAFAAQALAVTRDLGLPDDAEHVNPN 354
           V P IMG GP  A    LA AGL+  D+  IELNEAFAAQALAV RDL L  D   VNP+
Sbjct: 290 VPPEIMGIGPKEAIPAALAQAGLKQDDLKWIELNEAFAAQALAVARDLEL--DMSKVNPH 347

Query: 355 GGAIALGHPLGMSGARLVTTALNELERRHAAGQKARYALCTMCIGVGQGIALIIE 409
           GGAIALGHPLG +GA    T ++ +     AG K  + + TMCIG G G A IIE
Sbjct: 348 GGAIALGHPLGATGAIRTATLVHGM---RDAGLKG-HGMVTMCIGTGMGAAGIIE 398


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: 422
Number of extensions: 22
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: 400
Length adjustment: 31
Effective length of query: 384
Effective length of database: 369
Effective search space:   141696
Effective search space used:   141696
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