Aligments for a candidate for treF in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Aligments 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)



>lcl|FitnessBrowser__SB2B:6937506 Sama_1662 alpha amylase, catalytic
           region (RefSeq)
          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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 preprint 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

GapMind for catabolism of small carbon sources