Alignments for a candidate for susB in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for susB in Stenotrophomonas chelatiphaga DSM 21508

Align α-glucosidase (SusB;Aglu;BFO_2272) (EC 3.2.1.20) (characterized)
to candidate WP_057507039.1 ABB28_RS02145 alpha-glucosidase

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



>NCBI__GCF_001431535.1:WP_057507039.1
          Length = 684

 Score =  517 bits (1331), Expect = e-151
 Identities = 301/710 (42%), Positives = 407/710 (57%), Gaps = 65/710 (9%)

Query: 10  LFFLFSFLVSAPFTMRAEELKSPDGNLLMRFEVNGEGTPVYELTYKRKPVIKPSRLGLEI 69
           L  L +  V    T+ +  ++SP   L +  +V+G GT  Y++      V+  S+LG E+
Sbjct: 18  LLLLLASPVVLAATVPSASVESPGKILKVTLQVDG-GTARYQVQRLGDTVVDASKLGFEL 76

Query: 70  EGFSLRKAFTLKGVETVTFDETWTPVWGEVKAIRNHYNEMTATLHQADGDRTMV-IRFRL 128
               L + F + G  T  FDETW   WGE +  RNHYNE+T +L Q  GDR  + + FR+
Sbjct: 77  RDGRLDRDFEITGSSTRRFDETWEQPWGERRLTRNHYNELTVSLRQTTGDRRRLDVVFRV 136

Query: 129 YDDGLGFRYEFPQQKSLNYFVIKEEYSEFAMAGDHKAFWIP-GDYDTQEYDYTESRLTEI 187
           +DDG+GFRY FPQQ  L   +I EE +EFA+A    A+WIP G+    EY Y  + L E+
Sbjct: 137 FDDGVGFRYVFPQQPGLAEAIIDEELTEFAIAQHSTAWWIPAGEPIHYEYLYARTPLQEV 196

Query: 188 RGLMQTAITPNTSQTPFSPTGVQTALMMKSDDGLYINLHEAALVDYPCMSLN-LDDQTLT 246
             L  T IT                  ++SD GL++ +HEAALVDY  M L   D Q L 
Sbjct: 197 P-LAHTPIT------------------LRSDSGLHVAIHEAALVDYAGMWLRRTDGQRLR 237

Query: 247 FQSWLTPDAQGKKGYMQTPCHTPWRTVIVSDDARRILASHLTLNLNEPCKLDDVSWIRPV 306
            Q  L+P A+G K     P  TPWRT+ ++D A  ++ S L LNLNEP  L DVSW++P 
Sbjct: 238 AQ--LSPSAEGWKVRRALPFATPWRTLQIADRAGGLVESDLILNLNEPNALGDVSWVKPS 295

Query: 307 KYIGVWWEMISGKSTWAYTNDLPSVHLDVTDYTKMKPNGTHAANNEKVRRYIDFAAKHGF 366
           KY+GVWW M   + +WA                       HAA   K R+ IDFAA +GF
Sbjct: 296 KYLGVWWSMHLDEESWA-------------------TGPRHAATTAKTRKVIDFAAANGF 336

Query: 367 DQVLVEGWNIGWE-DWFGNSKDYVFDFVTPYPDFDLKALNEYAHSKGVKLMMHHETSSSV 425
             VLVEGWN GW+ +W GN  D  FDF    PDFD++AL+ Y   KGV L+ HHET  ++
Sbjct: 337 RGVLVEGWNPGWDGNWVGNGYD--FDFTRATPDFDIEALSAYGAKKGVHLVGHHETGCAI 394

Query: 426 RNYERQMEKAYKLMNDYGYNAVKSGYV---GNIIPRG--------EYHYGQWMVNHYLYA 474
            +YE Q+  A  L    G ++ K+GYV   G +  R         E+H GQ+M  H+L  
Sbjct: 395 DHYEDQLGAALDLYARLGVDSFKTGYVCDDGQVDRRNPAGGPLLREWHDGQFMARHHLKV 454

Query: 475 VKKAAEHRIMVNAHEAVRPTGLCRTYPNLIGNEAARGGEYESFGG--NKVFHTTILPFTR 532
           V++AA  R+ VN HE ++ TGL RTYPN +  E ARG EY ++G   N   H   L FTR
Sbjct: 455 VQEAAARRLAVNPHEPIKDTGLRRTYPNWVSREGARGMEYNAWGQPPNPPEHEVNLVFTR 514

Query: 533 LMGGPMDYTPGIFETRLEKVNPGNNSYVHSTLARQLALYVTMYSPLQMAADLPENYERFM 592
           ++ GPMDYTPG+   +       +   + STLARQLALYV +YSP+QMAADLPE+Y + +
Sbjct: 515 MLSGPMDYTPGVLSLKGR-----HGQAIPSTLARQLALYVVLYSPIQMAADLPEHYLQHL 569

Query: 593 DAFQFIKDVAIDWDDSKYLEAEPGRYITVARKAKGTNNWFVGCTANEDGHLSNVSLDFLD 652
           DAFQFIKDVA+DW+ S+ L+ E G ++T+ R+ + + +WF+G   +E G +  VSL FL+
Sbjct: 570 DAFQFIKDVAVDWEQSRVLDGEVGDFVTIVRRDRNSRDWFLGSITDEHGRVLPVSLGFLE 629

Query: 653 PGRKYTATIYADAPTAHYEKNPQAYTIKQMKVTNKSKLTLRAASGGGYAI 702
           PG +Y A IY D   A +  NP A+  +  +VT+   LTL    GGG AI
Sbjct: 630 PGVRYRAEIYRDGDGADFRSNPFAFARETREVTSADALTLVLGPGGGQAI 679


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: 1383
Number of extensions: 83
Number of successful extensions: 10
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: 684
Length adjustment: 39
Effective length of query: 669
Effective length of database: 645
Effective search space:   431505
Effective search space used:   431505
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 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