Alignments for a candidate for ams in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for ams in Phaeobacter inhibens BS107

Align Alpha-glucosidase; EC 3.2.1.- (characterized, see rationale)
to candidate GFF775 PGA1_c07890 putative alpha-glucosidase AglA

Query= uniprot:A8LLL3
         (552 letters)



>FitnessBrowser__Phaeo:GFF775
          Length = 552

 Score =  845 bits (2184), Expect = 0.0
 Identities = 391/551 (70%), Positives = 446/551 (80%), Gaps = 1/551 (0%)

Query: 1   MNAEAQMREVKSLAADPDWWRGAVIYQIYPRSFQDSNGDGIGDLLGIVERMPYIASLGVD 60
           MNA+AQ+   + LAADPDWWRGAVIYQIYPRS+QDSNGDGIGDL GI +R+P+IASLGVD
Sbjct: 1   MNAQAQLDPAQVLAADPDWWRGAVIYQIYPRSYQDSNGDGIGDLRGITQRLPHIASLGVD 60

Query: 61  AIWISPFFTSPMKDFGYDISDYFDVDPMFGSLADFDALIETAHMYGLRVMIDLVLSHTSD 120
           AIWISPFFTSPMKDFGYD+SDY DVDPMFGSL++FD L+  AH  GLRVMIDLVLSHTSD
Sbjct: 61  AIWISPFFTSPMKDFGYDVSDYCDVDPMFGSLSNFDQLVAAAHRLGLRVMIDLVLSHTSD 120

Query: 121 QHPWFEESRSSRDNPKADWYVWADAKPDGTPPNNWLSIFGGSGWHWDARRCQYYLHNFLT 180
           QH WF ESR SRDN +ADWYVWAD +PDGTPPNNWLSIFGGS W WD RR QYYLHNFL 
Sbjct: 121 QHAWFGESRQSRDNARADWYVWADPQPDGTPPNNWLSIFGGSAWQWDPRREQYYLHNFLV 180

Query: 181 SQPDLNFHCADVQDALLGVGRFWLDRGVDGFRLDTINFYVHDAELRDNPPLPPEERNSNI 240
           SQPDLNFH   VQDALL V RFWL+RGVDGFRLDTINFY HDAELR NP LPPE+RN+ I
Sbjct: 181 SQPDLNFHSPAVQDALLDVTRFWLERGVDGFRLDTINFYYHDAELRSNPALPPEQRNATI 240

Query: 241 APEVNPYNHQRHLYSKNQPENLEFLAKFRAMMEEYPAIAAVGEVGDAQYGLEILGQYTRG 300
           AP VNPYNHQ HLYSKNQPENL FL +FRA+++EYPA AAVGEVGDAQ GLEI+G YT  
Sbjct: 241 APSVNPYNHQEHLYSKNQPENLAFLGRFRALLDEYPAKAAVGEVGDAQRGLEIMGSYTAA 300

Query: 301 ETGVHMCYAFEFLAQEKLTAKRVAEVLNKVDEVASDGWACWAFSNHDVMRHVSRWDLTPG 360
            TGVHMCYAFE LA++ LTA R+AEV  +VD VA++GWACWAFSNHDV+RH SRW L P 
Sbjct: 301 NTGVHMCYAFELLAKDVLTASRLAEVFAEVDRVAANGWACWAFSNHDVIRHSSRWGLNPA 360

Query: 361 AQRGMLTLLMCLRGSVCLYQGEELGLPEAEVAFDDLQDPYGIEFWPEYKGRDGCRTPMVW 420
           AQR   T++MCLRG+ C+YQGEELGLPEA++AF+DLQDPYGIEFWPE+KGRDGCRTPMVW
Sbjct: 361 AQRLFTTMMMCLRGTTCIYQGEELGLPEADIAFEDLQDPYGIEFWPEFKGRDGCRTPMVW 420

Query: 421 QSDNMSGGFSIHRPWLPVSTEHLGLAVAVQEEAPDALLHHYRRALAFRRAHPALVKGDIS 480
           +  N SGGFS  +PWLPVS EHL L+VA QE  PDA+LHHYRRA+A R+AHPAL  G   
Sbjct: 421 EPSNGSGGFSAGKPWLPVSPEHLNLSVASQEADPDAMLHHYRRAIALRKAHPALAVGTHD 480

Query: 481 DVTVVGDVISFLRKDPEETVFVAINMSDAPGAVDLPPGNWMQIGAELNSGGTSPDG-RVH 539
            +   G+V  F R+D +E +F A N+ D P  + LP G W +   ++        G RV 
Sbjct: 481 QLRAEGNVAFFTRQDRDEVIFCAFNLGDIPAEITLPEGTWRKPDTDIALADLPQSGARVV 540

Query: 540 LGPWQPCIALK 550
           L PWQ C+A++
Sbjct: 541 LAPWQACLAVR 551


Lambda     K      H
   0.321    0.138    0.451 

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: 1155
Number of extensions: 36
Number of successful extensions: 2
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: 552
Length adjustment: 36
Effective length of query: 516
Effective length of database: 516
Effective search space:   266256
Effective search space used:   266256
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 (21.8 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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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