GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__ANA3:7025148
          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:

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