Alignments for a candidate for susB in Shewanella oneidensis MR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for susB in Shewanella oneidensis MR-1

Align α-glucosidase (SusB;Aglu;BFO_2272) (EC 3.2.1.20) (characterized)
to candidate 201594 SO2450 alpha-glucosidase (NCBI ptt file)

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



>FitnessBrowser__MR1:201594
          Length = 699

 Score =  492 bits (1267), Expect = e-143
 Identities = 281/708 (39%), Positives = 397/708 (56%), Gaps = 66/708 (9%)

Query: 15  SFLVSAPFTMRAEELKSPDGNLLMRFEVNGEGTPVYELTYKRKPVIKPSRLGLEIEGFS- 73
           S   SA    +   L SP+ ++ +    +  G   Y++ +  K +I+PSRLGL  +    
Sbjct: 33  SSFFSANLVAQTVTLSSPNQHIQISLS-DDTGRAEYKIDFHGKTIIEPSRLGLVFQSIGE 91

Query: 74  LRKAFTLKGVETVTFDETWTPVWGEVKAIRNHYNEMTATLHQADGDRTMVIRFRLYDDGL 133
           L +   +K     + D+ W   WGE + I++ +N+++  L   DG   + + F  +DDG+
Sbjct: 92  LGQGLRIKSSHITSTDDKWQQPWGEQEWIKDQHNQLSVVL--TDGKIDLNLEFNAFDDGI 149

Query: 134 GFRYEFPQQKSLNY---FVIKEEYSEFAMAGDHKA--FWIPG-DYDTQEYDYTESRLTEI 187
           GFRY   +Q +L       I +E +EF +   +KA  +WIP   ++  EY Y  S L ++
Sbjct: 150 GFRYHLAEQAALPVDTPLSITDELTEFNIGQSNKATAWWIPSRGWNRYEYLYRTSALNQV 209

Query: 188 RGLMQTAITPNTSQTPFSPTGVQTALMMKSDDGLYINLHEAALVDYPCMSLNLDDQTLTF 247
                     + + TPF+          +  DG ++++HEAALV++  M+L+   +    
Sbjct: 210 ----------DRAHTPFT---------FRLADGTHLSIHEAALVNFASMTLD-QQRDGKL 249

Query: 248 QSWLTPDAQGKKGYMQTPCHTPWRTVIVSDDARRILASHLTLNLNEPCKLDDVSWIRPVK 307
           ++ LTP + G +   Q   +TPWRT+ ++D A  +L SHL LNLNEP KL DVSWI+P K
Sbjct: 250 KADLTPWSDGIRVKTQAGFYTPWRTIQIADKATGLLNSHLILNLNEPNKLGDVSWIKPGK 309

Query: 308 YIGVWWEMISGKSTWAYTNDLPSVHLDVTDYTKMKPNGTHAANNEKVRRYIDFAAKHGFD 367
           Y+G+WW M   K+TW                        H A   + +RY+DFAAK+ FD
Sbjct: 310 YVGIWWGMHLNKNTWG-------------------SGPKHGATTSETKRYMDFAAKYHFD 350

Query: 368 QVLVEGWNIGWE-DWFGNSKDYVFDFVTPYPDFDLKALNEYAHSKGVKLMMHHETSSSVR 426
            VLVEGWN GW+ DWF N     F F   Y DFDL A+  Y   KGV+L+ HHET+ SV 
Sbjct: 351 GVLVEGWNQGWDGDWFHNGDQ--FSFTKAYDDFDLPAITAYGAKKGVRLIGHHETAGSVT 408

Query: 427 NYERQMEKAYKLMNDYGYNAVKSGYVG----------NIIPRGEYHYGQWMVNHYLYAVK 476
           +Y +QM  A+ L   +G   VK+GYV           N I R E+H GQ+MV  YLY V 
Sbjct: 409 HYRKQMADAFILYEKHGVTQVKTGYVADGGQIKRFDENGIMRHEWHDGQFMVGEYLYNVT 468

Query: 477 KAAEHRIMVNAHEAVRPTGLCRTYPNLIGNEAARGGEYESFGG--NKVFHTTILPFTRLM 534
           +AA+H I +N HE ++ TGL RTYPN I  E ARG EY ++G   N   HT +LPFTR++
Sbjct: 469 EAAKHHISINTHEPIKDTGLRRTYPNWISREGARGQEYNAWGSPPNSPEHTAMLPFTRML 528

Query: 535 GGPMDYTPGIFETRLEKVNPGNNSYVHSTLARQLALYVTMYSPLQMAADLPENYERFMDA 594
            GPMD+TPGIF+   + ++  N   V +TL +QLALYV +YSP+QMAADLP NY++ +DA
Sbjct: 529 AGPMDFTPGIFDLAPKGLDAENR--VQTTLMKQLALYVVLYSPIQMAADLPRNYQKHLDA 586

Query: 595 FQFIKDVAIDWDDSKYLEAEPGRYITVARKAKGTNNWFVGCTANEDGHLSNVSLDFLDPG 654
           FQFI+DV  DW  S  L  E G Y+  AR+AK   +W++G   +E      V LDFLDP 
Sbjct: 587 FQFIRDVPTDWYQSIALAGEVGDYVVFARQAKDQKDWYLGALTDETARKVTVKLDFLDPH 646

Query: 655 RKYTATIYADAPTAHYEKNPQAYTIKQMKVTNKSKLTLRAASGGGYAI 702
           ++Y A IY D   A ++ NP  Y I+  +V+ K  L L  AS  G AI
Sbjct: 647 KRYQAQIYRDGAKADWKTNPYDYVIETKEVSAKDSLNLALASSSGTAI 694


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: 1427
Number of extensions: 68
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: 699
Length adjustment: 39
Effective length of query: 669
Effective length of database: 660
Effective search space:   441540
Effective search space used:   441540
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 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