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_035132127.1 Q763_RS05915 glycoside hydrolase family 97 protein

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



>NCBI__GCF_000769915.1:WP_035132127.1
          Length = 665

 Score =  490 bits (1262), Expect = e-143
 Identities = 277/677 (40%), Positives = 383/677 (56%), Gaps = 46/677 (6%)

Query: 28  ELKSPDGNLLMRFEVNGEGTPVYELTYKRKPVIKPSRLGLEIEGFSLRKAFTLKGVETVT 87
           EL SP+G   + F +NG   P Y + ++ K +I PS LG  ++   L K F L  V+T T
Sbjct: 28  ELASPNGENKITFSLNGN-MPTYTVNHEEKEIITPSALGFVLKNEDLTKDFELVDVQTST 86

Query: 88  FDETWTPVWGEVKAIRNHYNEMTATLHQADGDRTMVIRFRLYDDGLGFRYEFPQQKSLNY 147
            D+TW  VWGE K IRNHYNEM   L Q+     + I+FR +DDG+ FRY FP+Q   + 
Sbjct: 87  HDDTWEQVWGEKKNIRNHYNEMVVKL-QSKEKHNLEIQFRAFDDGVAFRYVFPKQNIKDS 145

Query: 148 FVIKEEYSEFAMAGDHKAFWIPGDYDTQEYDYTESRLTEIRGLMQTAITPNTSQTPFSPT 207
             I +E + F +  D KA+WIP  Y    Y+Y           +  A   +T        
Sbjct: 146 IFIMDEVTAFNLKEDGKAWWIPA-YQENRYEY-----------LYEASPVSTLDV----- 188

Query: 208 GVQTALMMKSDDGLYINLHEAALVDYPCMSLNLDDQTLTFQSWLTPDAQGKKGYMQTPCH 267
            V T L +++ DG+ ++ HEA LVD+  M L   + +   +S L P A G K        
Sbjct: 189 -VHTPLTIENKDGIVVSFHEANLVDFASMVLRHTEGS-NLKSELVPWADGVKVRTTETFT 246

Query: 268 TPWRTVIVSDDARRILASHLTLNLNEPCKLDDVSWIRPVKYIGVWWEMISGKST-WAYTN 326
           +PWRT+ +      ++ S++ LNLNEP  L D S+I P KY G+WW M  GK T W   N
Sbjct: 247 SPWRTIQIGKKPGDLITSYMILNLNEPNALTDTSYIEPFKYTGIWWGMHIGKYTFWESEN 306

Query: 327 DLPSVHLDVTDYTKMKPNGTHAANNEKVRRYIDFAAKHGFDQVLVEGWNIGWEDWFGNSK 386
                                 A  +  + YIDF  K G + +L+EGWN GW   +  ++
Sbjct: 307 Q--------------------GATTKNAKEYIDFNNKEGINYLLIEGWNKGWTPAWYENR 346

Query: 387 DYVFDFVTPYPDFDLKALNEYAHSKGVKLMMHHETSSSVRNYERQMEKAYKLMNDYGYNA 446
            ++F F     +FDL+ + EY  SKGV ++ +HET S++ NY +++++ + L    G + 
Sbjct: 347 MHMFSFTENADNFDLEKVVEYGKSKGVNIIGYHETGSNLINYLKEIDEGFALYKRLGIHN 406

Query: 447 VKSGYVGNIIPRGEYHYGQWMVNHYLYAVKKAAEHRIMVNAHEAVRPTGLCRTYPNLIGN 506
           VK G VG+ +   E+H+GQ+ VN+Y Y +KKAAE+ + VN HE ++ TG  RTYPN++  
Sbjct: 407 VKIGQVGSKLNMKEWHHGQFGVNYYRYVLKKAAEYGLAVNFHEPIKDTGERRTYPNMMAR 466

Query: 507 EAARGGEYESFG-GNKVFHTTILPFTRLMGGPMDYTPGIFETRLEKVNPGNNSYVHSTLA 565
           E +RG EY ++  GN   H TILPFTRL+ GPMD+TPGI +  + +  PG    VH+T A
Sbjct: 467 EGSRGMEYNAWSEGNPPSHETILPFTRLLSGPMDFTPGILDVEVTQGYPGKR--VHTTAA 524

Query: 566 RQLALYVTMYSPLQMAADLPENYERFMDAFQFIKDVAIDWDDSKYLEAEPGRYITVARKA 625
           +QLALYVT+YSP+QM ADLPENYE    AFQF+KDV  DW+D+K L  E G YIT ARK 
Sbjct: 525 KQLALYVTIYSPIQMLADLPENYEG-NPAFQFLKDVPTDWEDTKVLNGEIGEYITTARKD 583

Query: 626 KGTNNWFVGCTANEDGHLSNVSLDFLDPGRKYTATIYADAPTAHYEKNPQAYTIKQMKVT 685
             + +W++G   NE      VSLDFLD   +Y A IYADA       NP   +I +  VT
Sbjct: 584 VHSADWYLGSITNEKARDLEVSLDFLDADAQYEAQIYADAEGTDETHNPAKVSITKQNVT 643

Query: 686 NKSKLTLRAASGGGYAI 702
            K KLTL+  + GG AI
Sbjct: 644 AKDKLTLKLGASGGTAI 660


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: 1389
Number of extensions: 78
Number of successful extensions: 8
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: 665
Length adjustment: 39
Effective length of query: 669
Effective length of database: 626
Effective search space:   418794
Effective search space used:   418794
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.

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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 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