Alignments for a candidate for susB in Flavobacterium beibuense F44-8

GapMind for catabolism of small carbon sources

Alignments for a candidate for susB in Flavobacterium beibuense F44-8

Align α-glucosidase (SusB;Aglu;BFO_2272) (EC 3.2.1.20) (characterized)
to candidate WP_035130186.1 Q763_RS01135 glycoside hydrolase family 97 protein

Query= CAZy::AEW20125.1
         (708 letters)



>NCBI__GCF_000769915.1:WP_035130186.1
          Length = 673

 Score =  522 bits (1345), Expect = e-152
 Identities = 288/710 (40%), Positives = 402/710 (56%), Gaps = 57/710 (8%)

Query: 6   LRKKLF------FLFSFLVSAPFTMRAEELKSPDGNLLMRFEVNGEGTPVYELTYKRKPV 59
           ++ KLF      F    ++S     +   + SP     + F++  +G P Y  +   K V
Sbjct: 1   MKNKLFRLCLTAFASVMVLSCGTEEKVYTISSPGNTNELVFKLTEKGEPQYSFSSNGKTV 60

Query: 60  IKPSRLGLEI-EGFSLRKAFTLKGVETVTFDETWTPVWGEVKAIRNHYNEMTATLHQADG 118
           I+PS +G E  E   +   F +   E  + DE W   WGE K +R+++ E+   L ++ G
Sbjct: 61  IEPSLMGFEFQEANKMTDGFEVVNTEEKSVDENWDQPWGEFKTVRDNHKELVVHLKESKG 120

Query: 119 D-RTMVIRFRLYDDGLGFRYEFPQQKSLNYFVIKEEYSEFAMAGDHKAFWIPGDYDTQEY 177
           D R M I FR++DDGLGFRY FP+Q ++    I +E ++F    D+  +WIP   +   Y
Sbjct: 121 DGRLMDIIFRVFDDGLGFRYYFPEQPNMGEVKIADEVTQFTFPFDNDVWWIPVHSENSYY 180

Query: 178 DYTESRLTEIRGLMQTAITPNTSQTPFSPTG-VQTALMMKSDDGLYINLHEAALVDYPCM 236
           +    +                  TP S T  + T    ++ D L++ +HEA L D+  M
Sbjct: 181 ESFYRK------------------TPISKTDTINTPATFETKDSLFVAIHEANLTDFASM 222

Query: 237 SLNLDDQTLTFQSWLTPDAQGKKGYMQTPCHTPWRTVIVSDDARRILASHLTLNLNEPCK 296
           +L L     +++S L P A G K Y +TP  TPWRTV+V   A  +  S LTLNLNEPCK
Sbjct: 223 TL-LKTNGNSYKSDLVPWADGVKVYAKTPFQTPWRTVMVGIKAGDLAMSTLTLNLNEPCK 281

Query: 297 LDDVSWIRPVKYIGVWWEMISGKSTWAYTNDLPSVHLDVTDYTKMKPNGTHAANNEKVRR 356
           ++D SWI P+KY+G+WW M   K TW                        H A  E  ++
Sbjct: 282 IEDTSWITPMKYVGIWWGMHLDKYTWGQGE-------------------IHGATTENTKK 322

Query: 357 YIDFAAKHGFDQVLVEGWNIGWE-DWFGNSKDYVFDFVTPYPDFDLKALNEYAHSKGVKL 415
           YIDFAA +GFD VLVEGWN GW+ DW  +     F FV PYPDFDL+ +  YA +K V+L
Sbjct: 323 YIDFAAANGFDGVLVEGWNEGWDGDWTADGT--AFSFVKPYPDFDLEEITRYAAAKNVRL 380

Query: 416 MMHHETSSSVRNYERQMEKAYKLMNDYGYNAVKSGYVGNIIPRGEYHYGQWMVNHYLYAV 475
           + HHET+ +  +YE Q+E AY L N  G N+VK+GYV   + + E+H  Q+ V HY   +
Sbjct: 381 IGHHETAGAASHYESQLEDAYSLYNKVGVNSVKTGYVNKYLDKKEWHDSQFGVRHYRKVI 440

Query: 476 KKAAEHRIMVNAHEAVRPTGLCRTYPNLIGNEAARGGEYESF---GGNKVFHTTILPFTR 532
           + AA+H IM++ HE V+ TGL RTYPNL+  E ARG EY ++   GGN   HTTI+PFTR
Sbjct: 441 ETAAKHHIMIDNHEPVKGTGLWRTYPNLMAQEGARGQEYNAWSADGGNTPEHTTIMPFTR 500

Query: 533 LMGGPMDYTPGIFETRLEKVNPGNNSYVHSTLARQLALYVTMYSPLQMAADLPENYERFM 592
           ++ GP D+TPG F    E     N + V +T+A+QLALYV ++SPLQMA+DLPENY+   
Sbjct: 501 MLAGPFDFTPGNFNFDYE---TPNKAMVQTTVAKQLALYVVLFSPLQMASDLPENYKGRA 557

Query: 593 DAFQFIKDVAIDWDDSKYLEAEPGRYITVARKAKGTNNWFVGCTANEDGHLSNVSLDFLD 652
           + FQFIKDV  +W++SK L+++ G Y+T+ARK + +  WF+G   N D     V L+FL 
Sbjct: 558 E-FQFIKDVPCNWEESKVLDSKIGEYVTIARKDRNSEEWFLGSITNSDARKIAVPLNFLK 616

Query: 653 PGRKYTATIYADAPTAHYEKNPQAYTIKQMKVTNKSKLTLRAASGGGYAI 702
            G  Y A IY D   A Y++NP   +I  M V + S L L  A GGG A+
Sbjct: 617 QGVPYKAEIYRDGEGADYKENPYPVSIDVMTVNSTSVLDLNLAPGGGTAV 666


Lambda     K      H
   0.319    0.135    0.417 

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: 1490
Number of extensions: 90
Number of successful extensions: 9
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: 708
Length of database: 673
Length adjustment: 39
Effective length of query: 669
Effective length of database: 634
Effective search space:   424146
Effective search space used:   424146
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 (21.7 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Sep 24 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 2024 update 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