Alignments for a candidate for susB in Shewanella loihica PV-4

GapMind for catabolism of small carbon sources

Alignments for a candidate for susB in Shewanella loihica PV-4

Align α-glucosidase (SusB;Aglu;BFO_2272) (EC 3.2.1.20) (characterized)
to candidate 5209405 Shew_1876 alpha-glucosidase (RefSeq)

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



>FitnessBrowser__PV4:5209405
          Length = 707

 Score =  505 bits (1300), Expect = e-147
 Identities = 286/695 (41%), Positives = 402/695 (57%), Gaps = 67/695 (9%)

Query: 29  LKSPDGNLLMRFEVNGEGTPVYELTYKRKPVIKPSRLGLEIEGFS-LRKAFTLKGVETVT 87
           L SPD  +++    + + TP Y +++  K VI+PS+LG+  E        F+++ V+   
Sbjct: 54  LTSPDKQIVVSLS-DDDQTPRYSVSFHGKKVIEPSKLGIVFESLGEFGTDFSIQEVKRSQ 112

Query: 88  FDETWTPVWGEVKAIRNHYNEMTATLHQADGDRTMVIRFRLYDDGLGFRYEFPQQKSLNY 147
            DE W   WGE + + + +N +TATL  ++G    V+ F+++DDGLGFRY+ P+Q  L+ 
Sbjct: 113 ADERWQQPWGEREWVVDKHNGLTATL--SNGQYRFVVEFKVFDDGLGFRYQMPKQGDLDK 170

Query: 148 FVIKEEYSEFAMAGDHK--AFWIPG-DYDTQEYDYTESRLTEIRGLMQTAITPNTSQTPF 204
             I  E +EF +       A+WIP   ++  EY Y ++ L ++          +   TPF
Sbjct: 171 LNITSELTEFTLPQPENVTAWWIPARGWNRYEYLYQKTPLKQV----------DRVHTPF 220

Query: 205 SPTGVQTALMMKSDDGLYINLHEAALVDYPCMSLNLDDQTLTFQSWLTPDAQGKKGYMQT 264
           + T           DG+++++HEAALVDY  M+L+   +  T ++ LTP + G +   Q 
Sbjct: 221 TFT---------LSDGVHMSIHEAALVDYAAMTLD-QRRDGTLRADLTPWSDGMRVKTQA 270

Query: 265 PCHTPWRTVIVSDDARRILASHLTLNLNEPCKLDDVSWIRPVKYIGVWWEMISGKSTWAY 324
              TPWRT+ ++D A  +L S L LNLNEP KL DV W+ P KY+G+WW M   ++TW  
Sbjct: 271 GFSTPWRTIQIADKATGLLNSDLILNLNEPNKLGDVDWVEPGKYVGIWWGMHLNENTWG- 329

Query: 325 TNDLPSVHLDVTDYTKMKPNGTHAANNEKVRRYIDFAAKHGFDQVLVEGWNIGWE-DWFG 383
                                 H A   + +RY+DFAA++GF  VLVEGWNIGW+  WF 
Sbjct: 330 ------------------SGDKHGATTSETKRYMDFAAENGFAGVLVEGWNIGWDGSWFH 371

Query: 384 NSKDYVFDFVTPYPDFDLKALNEYAHSKGVKLMMHHETSSSVRNYERQMEKAYKLMNDYG 443
           N    VF F   YPDFDL  ++ Y  SKGV+L+ HHETS SV NY +QM  AY L   YG
Sbjct: 372 NGD--VFSFTQAYPDFDLPEISAYGASKGVRLIGHHETSGSVTNYRKQMSDAYDLYQQYG 429

Query: 444 YNAVKSGYV---GNI-------IPRGEYHYGQWMVNHYLYAVKKAAEHRIMVNAHEAVRP 493
              VK+GYV   G+I       I R E+H GQ+MVN YL++V +AA+  I +N HE ++ 
Sbjct: 430 VTQVKTGYVADGGDIKRVDEQGIVRHEWHDGQFMVNEYLHSVTEAAKRHISINTHEPIKD 489

Query: 494 TGLCRTYPNLIGNEAARGGEYESFGG--NKVFHTTILPFTRLMGGPMDYTPGIFETRLEK 551
           TGL RTYPN I  E ARG E+ ++G   N   HTT L +TR++ GPMD+TPGIF+   + 
Sbjct: 490 TGLRRTYPNWIAREGARGQEFNAWGTPPNNPSHTTTLAYTRMLAGPMDFTPGIFDLAPKG 549

Query: 552 VNPGNNSYVHSTLARQLALYVTMYSPLQMAADLPENYERFMDAFQFIKDVAIDWDDSKYL 611
           ++  N   V +TL +QLALYV +YSP+QMAADLP NY++  DAF+FI+DV  DW  S  L
Sbjct: 550 LDAVNR--VQTTLTKQLALYVVLYSPIQMAADLPRNYKQHPDAFKFIRDVPTDWAQSIAL 607

Query: 612 EAEPGRYITVARKAKG----TNNWFVGCTANEDGHLSNVSLDFLDPGRKYTATIYADAPT 667
             E G Y+  AR+ +G      +W++G   ++D    N+ LDFLDP   Y   IY D   
Sbjct: 608 AGEVGEYVAFARQERGGKSQGKDWYLGAITDDDAREINIKLDFLDPALSYEVQIYRDGDK 667

Query: 668 AHYEKNPQAYTIKQMKVTNKSKLTLRAASGGGYAI 702
           A +  NP  Y I+  KV +K +LTL+ AS GG AI
Sbjct: 668 ADWRTNPYDYVIETQKVNSKQQLTLKLASSGGVAI 702


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: 1469
Number of extensions: 84
Number of successful extensions: 11
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: 707
Length adjustment: 39
Effective length of query: 669
Effective length of database: 668
Effective search space:   446892
Effective search space used:   446892
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: 55 (25.8 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