GapMind for catabolism of small carbon sources

 

Aligments for a candidate for treF in Shewanella sp. ANA-3

Align Putative alpha-glucosidase AglA (characterized, see rationale)
to candidate 7025148 Shewana3_2311 alpha amylase, catalytic region (RefSeq)

Query= uniprot:I7EUW4
         (552 letters)



>lcl|FitnessBrowser__ANA3:7025148 Shewana3_2311 alpha amylase,
           catalytic region (RefSeq)
          Length = 540

 Score =  568 bits (1463), Expect = e-166
 Identities = 265/500 (53%), Positives = 343/500 (68%), Gaps = 5/500 (1%)

Query: 19  WWRGAVIYQIYPRSYQDSNGDGIGDLRGITQRLPHIASLGVDAIWISPFFTSPMKDFGYD 78
           WWRGAVIYQIYPRS  D+NGDG+GDLRGI  +L +IASL VDAIWISPFF SPM DFGYD
Sbjct: 6   WWRGAVIYQIYPRSLLDTNGDGVGDLRGIITKLDYIASLNVDAIWISPFFKSPMADFGYD 65

Query: 79  VSDYCDVDPMFGSLSNFDQLVAAAHRLGLRVMIDLVLSHTSDQHAWFGESRQSRDNARAD 138
           +SDY +VDP+FG++ +FD+L+  AH+ G++V+ID VLSHTSDQHAWF ESR+SR N +AD
Sbjct: 66  ISDYREVDPLFGTMQDFDELIEKAHQRGIKVIIDQVLSHTSDQHAWFCESRESRTNPKAD 125

Query: 139 WYVWADPQPDGTPPNNWLSIFGGSAWQWDPRREQYYLHNFLVSQPDLNFHSPAVQDALLD 198
           WYVWA+P+ DGT PNNWL+IFGG AW+W+PRR+QYYLHNFL SQPD+NFH+P V+ A+LD
Sbjct: 126 WYVWAEPKEDGTAPNNWLAIFGGCAWEWEPRRQQYYLHNFLRSQPDINFHNPDVRQAVLD 185

Query: 199 VTRFWLERGVDGFRLDTINFYYHDAELRSNPALPPEQRNATIAPSVNPYNHQEHLYSKNQ 258
              FWL++GVDGFRLD I F YHD +LR NP  P ++R        NPY +Q H Y+ ++
Sbjct: 186 NVEFWLKKGVDGFRLDAITFCYHDEQLRDNPPKPKDKRQGRGFSEDNPYAYQYHYYNNDR 245

Query: 259 PENLAFLGRFRALLDEYPAKAAVGEVGDAQRGLEIMGSYTAANTGVHMCYAFELLAKDVL 318
           P+ + F+   R L++ YP    +GEV  A+  L +M +YT     +HM Y+FELL  D  
Sbjct: 246 PQTILFIEELRQLINRYPGAVTLGEV-SAEDSLAVMAAYTKGEDRLHMAYSFELLTDD-Y 303

Query: 319 TASRLAEVFAEVDRVAANGWACWAFSNHDVIRHSSRWGLNPAAQ---RLFTTMMMCLRGT 375
           +A+ + +    ++    +GW CWA  NHD  R +SRWG         ++   M+  LRG+
Sbjct: 304 SAAYIRQTVEALEASIGDGWPCWAIGNHDAQRVASRWGRGKQTSDMVKMLNAMVNSLRGS 363

Query: 376 TCIYQGEELGLPEADIAFEDLQDPYGIEFWPEFKGRDGCRTPMVWEPSNGSGGFSAGKPW 435
            C YQGEELGL EA I + +LQDP+G  FWP FKGRDGCRTPM WE +    GFS   PW
Sbjct: 364 VCSYQGEELGLTEAPIEYHELQDPFGKTFWPMFKGRDGCRTPMPWEQNADFSGFSQVTPW 423

Query: 436 LPVSPEHLNLSVASQEADPDAMLHHYRRAIALRKAHPALAVGTHDQLRAEGNVAFFTRQD 495
           LP++  H  L+V  QEAD  +MLH YR+ +A RK +PAL  G  + L A   +  F R  
Sbjct: 424 LPIAQAHRALAVDVQEADSQSMLHGYRQFLAWRKGYPALVEGEIEFLDAPEPLLVFVRTS 483

Query: 496 RDEVIFCAFNLGDIPAEITL 515
            ++ +   FNL D    ++L
Sbjct: 484 GEQKLLVCFNLQDTEQALSL 503


Lambda     K      H
   0.321    0.137    0.444 

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: 914
Number of extensions: 40
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: 552
Length of database: 540
Length adjustment: 35
Effective length of query: 517
Effective length of database: 505
Effective search space:   261085
Effective search space used:   261085
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.6 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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