GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Amantichitinum ursilacus IGB-41

Align Beta-ketoadipyl CoA thiolase (EC 2.3.1.-) (characterized)
to candidate WP_053936560.1 WG78_RS04410 acetyl-CoA C-acyltransferase

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



>NCBI__GCF_001294205.1:WP_053936560.1
          Length = 401

 Score =  302 bits (773), Expect = 1e-86
 Identities = 191/418 (45%), Positives = 243/418 (58%), Gaps = 34/418 (8%)

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

Query: 66  AGEDNRDVARMSLLLAGLPVDVPGSTINRLCGSGMDAVGSAARAIRTGETQLMIAGGVES 125
             E   +VAR+ LLLAGLP  V G TINR C SG++AV  AA  IR GE  +MIA G ES
Sbjct: 65  EAEQGMNVARIGLLLAGLPETVGGVTINRFCSSGVNAVAMAADRIRVGEADVMIAAGTES 124

Query: 126 MSRAPFVMGKADSAFSRKAEIF--DTTIGWRFVNPVLKKQYGIDSMPETAENVAADFGIS 183
           MS  P +  K     +   EIF  D  +G  F             M  TAE VA  + +S
Sbjct: 125 MSMVPMMGNKV----ALNPEIFAKDENLGIAF------------GMGLTAEKVAEQWKVS 168

Query: 184 REDQDAFALRSQQRTAAAQKEGRLAAEITPVTIPRRKQD---------PLVVDTDEHPR- 233
           REDQDAFA+ S +R  AA + G+ A EITP+    R  +            + TDE PR 
Sbjct: 169 REDQDAFAVESHRRALAAIEGGKFADEITPLEATYRVPNLATGEVEYIKKTLTTDEGPRR 228

Query: 234 ETSLEKLASLPTPFRENGTVTAGNASGVNDGACALLLAGADALKQYNLKPRARVVAMATA 293
           +TS+E LA L T F   G+VTAGN+S ++DGA A++L     LK+YNL P A+ V+ A  
Sbjct: 229 DTSMEGLAKLKTVFAAKGSVTAGNSSQMSDGAGAVILVSERILKEYNLTPLAKFVSFAVK 288

Query: 294 GVEPRIMGFGPAPATRKVLATAGLELADMDVIELNEAFAAQALAVTRDLGLPDDAEHVNP 353
           GV P IMG GP  A    L  AGL   D+  IELNEAFAAQ+LAV RDL L  D   +NP
Sbjct: 289 GVPPSIMGIGPKEAIPAALRVAGLNQDDLAWIELNEAFAAQSLAVIRDLNL--DTSKINP 346

Query: 354 NGGAIALGHPLGMSGARLVTTALNELERRHAAGQKARYALCTMCIGVGQGIALIIERM 411
            GGAIALGHPLG +GA    T ++ + R   AG   +Y + TMCIG G G A II+ +
Sbjct: 347 QGGAIALGHPLGATGAIRAATLVHGMRREGMAG---KYGMITMCIGTGMGAAGIIQSL 401


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: 447
Number of extensions: 27
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: 401
Length adjustment: 31
Effective length of query: 384
Effective length of database: 370
Effective search space:   142080
Effective search space used:   142080
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