GapMind for catabolism of small carbon sources

 

Alignments for a candidate for treF in Shewanella amazonensis SB2B

Align Putative alpha-glucosidase AglA (characterized, see rationale)
to candidate 6937506 Sama_1662 alpha amylase, catalytic region (RefSeq)

Query= uniprot:I7EUW4
         (552 letters)



>FitnessBrowser__SB2B:6937506
          Length = 544

 Score =  605 bits (1560), Expect = e-177
 Identities = 285/505 (56%), Positives = 354/505 (70%), Gaps = 9/505 (1%)

Query: 19  WWRGAVIYQIYPRSYQDSNGDGIGDLRGITQRLPHIASLGVDAIWISPFFTSPMKDFGYD 78
           WWRGA IYQIYPRS +DSNGDGIGDL+GI +RL +IASL VDAIWISPFF SPMKDFGYD
Sbjct: 6   WWRGAAIYQIYPRSLKDSNGDGIGDLQGIIERLDYIASLNVDAIWISPFFRSPMKDFGYD 65

Query: 79  VSDYCDVDPMFGSLSNFDQLVAAAHRLGLRVMIDLVLSHTSDQHAWFGESRQSRDNARAD 138
           +SDY DVDPMFG++ +FD+L+A AH LGL+V+ID VLSHTSD+HAWF ESRQSRDN +AD
Sbjct: 66  ISDYLDVDPMFGTMDDFDELIAKAHSLGLKVVIDQVLSHTSDEHAWFAESRQSRDNPKAD 125

Query: 139 WYVWADPQPDGTPPNNWLSIFGGSAWQWDPRREQYYLHNFLVSQPDLNFHSPAVQDALLD 198
           WYVWADP+ DGTPPNNWL+IFGG AW+W+PRR+QYYLHNFL SQPDLNFH  AV+ A+L+
Sbjct: 126 WYVWADPREDGTPPNNWLAIFGGCAWEWEPRRQQYYLHNFLKSQPDLNFHCEAVRQAVLN 185

Query: 199 VTRFWLERGVDGFRLDTINFYYHDAELRSNPALPPEQRNATIAPSVNPYNHQEHLYSKNQ 258
              FWL++GVDGFRLD I F +HD  LR NPA P ++R        NPY +Q H Y+  +
Sbjct: 186 NVEFWLKKGVDGFRLDAITFCFHDKALRDNPAKPADKRQGRGFSEDNPYAYQYHWYNNER 245

Query: 259 PENLAFLGRFRALLDEYPAKAAVGEVGDAQRGLEIMGSYTAANTGVHMCYAFELLAKDVL 318
           PE L F+   RAL+D YP    +GEV  ++  L  M  YT  +  +HM Y+FELL KD  
Sbjct: 246 PETLGFIEDLRALIDRYPGAVTLGEV-SSEDSLATMAEYTRGDNRLHMAYSFELLTKD-Y 303

Query: 319 TASRLAEVFAEVDRVAANGWACWAFSNHDVIRHSSRWGL---NPAAQRLFTTMMMCLRGT 375
           +A  +      ++    +GW CWA  NHDV R  SRWG     P   ++ + M+ CLRG+
Sbjct: 304 SAGYIRSTVEALEGAIGDGWPCWAIGNHDVERVISRWGQGKGTPQMAKMLSAMLGCLRGS 363

Query: 376 TCIYQGEELGLPEADIAFEDLQDPYGIEFWPEFKGRDGCRTPMVWEPSNGSGGF----SA 431
            C+YQGEELGL EADI F+ LQDP+GI FWP FKGRDGCRTPM W+      GF    S 
Sbjct: 364 LCVYQGEELGLTEADIPFDALQDPFGIAFWPNFKGRDGCRTPMPWQAEGEYMGFGATASG 423

Query: 432 GKPWLPVSPEHLNLSVASQEADPDAMLHHYRRAIALRKAHPALAVGTHDQLRAEGNVAFF 491
             PWLP+  EH  L+VA+Q A+PD++L+ + R +A R+  PAL  G    + ++  V  F
Sbjct: 424 AMPWLPLPEEHRALNVAAQSANPDSVLNQFSRFMAWRRTQPALVTGEIKFIDSKEPVLAF 483

Query: 492 TRQDRDEVIFCAFNLGDIPAEITLP 516
            R   D+ + C FNL D P  +T+P
Sbjct: 484 ERVSSDKKVLCVFNLSDKPQTMTVP 508


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: 1019
Number of extensions: 50
Number of successful extensions: 5
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: 544
Length adjustment: 36
Effective length of query: 516
Effective length of database: 508
Effective search space:   262128
Effective search space used:   262128
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: 53 (25.0 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