Alignments for a candidate for treF in Cereibacter sphaeroides ATCC 17029

GapMind for catabolism of small carbon sources

Alignments for a candidate for treF in Cereibacter sphaeroides ATCC 17029

Align Putative alpha-glucosidase AglA (characterized, see rationale)
to candidate WP_011840128.1 RSPH17029_RS00200 DUF3459 domain-containing protein

Query= uniprot:I7EUW4
         (552 letters)



>NCBI__GCF_000015985.1:WP_011840128.1
          Length = 536

 Score =  596 bits (1536), Expect = e-175
 Identities = 285/502 (56%), Positives = 352/502 (70%), Gaps = 9/502 (1%)

Query: 18  DWWRGAVIYQIYPRSYQDSNGDGIGDLRGITQRLPHIASLGVDAIWISPFFTSPMKDFGY 77
           DWWRG+V YQIYPRS+QDS+GDG+GDLRGI +RL H+A LG DAIW+SP F SPM+D GY
Sbjct: 3   DWWRGSVTYQIYPRSFQDSDGDGVGDLRGIIERLDHVAWLGADAIWLSPIFPSPMEDMGY 62

Query: 78  DVSDYCDVDPMFGSLSNFDQLVAAAHRLGLRVMIDLVLSHTSDQHAWFGESRQSRDNARA 137
           DVSDY  + P+FGS+ +FD L+A AH LGL+V+ID VLSH+S  H +F ESR+SRDN +A
Sbjct: 63  DVSDYTAIHPLFGSMEDFDALLARAHELGLKVIIDQVLSHSSSAHPFFRESRRSRDNPKA 122

Query: 138 DWYVWADPQPDGTPPNNWLSIFGGSAWQWDPRREQYYLHNFLVSQPDLNFHSPAVQDALL 197
           DWYVWAD QPDG+PPNNWLS+FGGSAW+WD +R QYYLHNFL+SQPD NFH+P VQD LL
Sbjct: 123 DWYVWADAQPDGSPPNNWLSVFGGSAWEWDAQRRQYYLHNFLISQPDFNFHNPEVQDWLL 182

Query: 198 DVTRFWLERGVDGFRLDTINFYYHDAELRSNPALPPEQRNATIAPSVNPYNHQEHLYSKN 257
           D  RFWL+RGVDGFRLDT+NFY+HDAELRSN    P  +N  I P VN Y+ Q+H +SK+
Sbjct: 183 DQMRFWLDRGVDGFRLDTVNFYFHDAELRSN---RPNPQNGPI-PPVNAYDMQDHAFSKS 238

Query: 258 QPENLAFLGRFRALLDEYPAKAAVGEVGDAQRGLEIMGSYTAANTGVHMCYAFELLAKDV 317
           + EN+AFL R R LLD+YP +A VGEV D  RGL IM  YT+    +HM Y FE+L++  
Sbjct: 239 RIENIAFLLRMRKLLDDYPDRAMVGEVADGLRGLAIMAEYTSGADRLHMAYTFEMLSR-T 297

Query: 318 LTASRLAEVFAEVDRVAANGWACWAFSNHDVIRHSSRW---GLNPAAQRLFTTMMMCLRG 374
            TA        E    A +GW CWAFSNHDV+RH++RW   G      RL   M++   G
Sbjct: 298 FTAGHFRSRIEEFFATAPHGWPCWAFSNHDVVRHATRWAGHGAEDDVARLAAAMLLSFEG 357

Query: 375 TTCIYQGEELGLPEADIAFEDLQDPYGIEFWPEFKGRDGCRTPMVWEPSNGSGGFSAGKP 434
           +  +YQGEELG  E ++ +E+L DP G+ FWPE KGRDGCRTPMVW+    +GGF+ G P
Sbjct: 358 SVSLYQGEELGQTETELLYEELTDPPGLRFWPEEKGRDGCRTPMVWD-DGPAGGFTTGTP 416

Query: 435 WLPVSPEHLNLSVASQEADPDAMLHHYRRAIALRKAHPALAVGTHDQLRAEGNVAFFTRQ 494
           WLPV P  L  +VASQ+  P ++L  YR  +  R+  PAL  G          +  FTR 
Sbjct: 417 WLPVKPPQLARNVASQKGIPGSVLETYRALLQFRRTQPALIRGRSRFFDLPEPMLGFTRT 476

Query: 495 DRDEVIFCAFNLGDIPAEITLP 516
              + + C FNLG  P   TLP
Sbjct: 477 LDGQSLACFFNLGIEPVSATLP 498


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: 1071
Number of extensions: 60
Number of successful extensions: 6
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: 536
Length adjustment: 35
Effective length of query: 517
Effective length of database: 501
Effective search space:   259017
Effective search space used:   259017
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 Apr 10 2024. The underlying query database was built on Sep 17 2021.

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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