Alignments for a candidate for susB in Shewanella amazonensis SB2B

GapMind for catabolism of small carbon sources

Alignments for a candidate for susB in Shewanella amazonensis SB2B

Align alpha-glucosidase (EC 3.2.1.20) (characterized)
to candidate 6935941 Sama_0156 glycosyl hydrolase family 31 protein (RefSeq)

Query= BRENDA::Q8RDL1
         (751 letters)



>FitnessBrowser__SB2B:6935941
          Length = 1108

 Score =  172 bits (435), Expect = 1e-46
 Identities = 115/342 (33%), Positives = 179/342 (52%), Gaps = 21/342 (6%)

Query: 420 ATKEGLLKERTNERPFILTRAAFAGIQRYAAMWTGDNRSLYEHLLMMMPMLMNVGLSGQP 479
           A  +G+L + ++ RPF+ T   +AG+QRYA  WTGD    ++++   +P L+  GLSGQ 
Sbjct: 395 AAADGIL-DNSDSRPFLWTVMGWAGMQRYAVTWTGDQSGSWDYIRWHIPTLIGSGLSGQA 453

Query: 480 FAGADVGGFEGDCSEELFIRWIEAAVFTPFLRVHSAIG-TKDQEPWSFGKKAEDIARKFI 538
           +A  DV    G  S E F R ++   FTP L   S       + PW F +    I R ++
Sbjct: 454 YATGDVDAIFGG-SPETFTRDLQWKAFTPVLMGMSGWSKAARKHPWWFDEPYRSINRDYL 512

Query: 539 KIRYELLPYIYDLFYEASKKGYPVMRPLVFEYQEDEN----THKIYDEFMLGQNLLIAPV 594
           K++  L PY+Y   +E  + G P++R L+++Y +D N     HK   +F+LG+++L+APV
Sbjct: 513 KLKMRLTPYMYTTAFETEQTGAPIVRGLMWDYNDDPNANTEAHKY--QFLLGKDMLVAPV 570

Query: 595 Y---LPSKD-RREVYLPSGIWYDYFMG---ERYEGGNYYLVEAPIDTIPVFVKEGAIIVK 647
           Y     SK  R +VYLP G W DY+ G   +  EGG     +  ++TIPVFV+ GAII  
Sbjct: 571 YRSQTASKGWREDVYLPKGQWIDYWDGRVVDAPEGGASIDYQVDLNTIPVFVRAGAIIPM 630

Query: 648 QKPLSYVEEDRIEEKVVEIYRGNRGRYVHYEDDGKTFDYKKGVY--NLFEI---EFEYFD 702
                Y      +   ++IY      Y+ YEDDG T  Y++G +   LF +   E +  D
Sbjct: 631 YPEALYDGHKPKDVLTLDIYPYGESEYLMYEDDGNTRRYQQGEFARQLFAVKAHEGKAGD 690

Query: 703 GEIDIKFDKVHFGYEDGAKKYRFVLKNFDEVKKVKINGEEVE 744
            E+ I   +  F  +D  + Y   L    +   V +NG++++
Sbjct: 691 IEVSIGAAEGKFDGQDEERVYELWLHTRTKPDSVLLNGKKLK 732



 Score = 48.5 bits (114), Expect = 2e-09
 Identities = 63/337 (18%), Positives = 128/337 (37%), Gaps = 56/337 (16%)

Query: 11  VRSEGKKLELRVITDKIVNIFVTDKE--------------EKRRDTIAIEKKKYDIPDFN 56
           +R EG  +++R  +  +V + V                  E  +    + K  Y    + 
Sbjct: 46  LRQEGASVDIRTDSGALVQVSVLKPSLIRIQAGANGKLTAEGSKAAAIVIKDDYPAVAYT 105

Query: 57  VEESKDKVLVLTKDLKVEIDKKTFFITFKDKDGDVINEDYGEGVKLGDSE-VRCYKKLRE 115
           + +  D  L+ T+ L + I +          D   +  +  + ++LG+S  V+      +
Sbjct: 106 LSDEGDYRLLKTEALALRIYEAPLRFALYQADNQTLITEELQSLELGESSTVQTLSTDVD 165

Query: 116 DHFYGFGEKAGYLDKKGEKFEMWNTDEFMTHNQTTKLLYESYPFFIGMNKKHTYGIFLDN 175
           + F+G G++ G  + KG+  E+  +  +   ++ +       PF++       YG+  + 
Sbjct: 166 ERFFGGGQQNGAFEFKGKSLEISYSGGWEEGDRPSPA-----PFYLSSKG---YGVLRNT 217

Query: 176 SFRSFFNMGEESEEYYYFGAYGGQMNYYFIYGNDIKEVVENYTYLTGRIELPPLWAL--- 232
                ++    S +    G    + + +F     I++V+ +YT LTGR  L P WA    
Sbjct: 218 WANGSYDF--RSSDALRLGHDEARFDAFFFAPGSIQQVLADYTELTGRARLIPRWAFEYG 275

Query: 233 -------GNQQSRYSYTPQ-----------EKVLEVAKTFREKDIPCDVIYLDIDYMEGY 274
                  G+   +    P            + +  VAK +RE D+P   I  +  Y  GY
Sbjct: 276 DADCYNDGDNVKKPGTVPDGWSDGPTGTTPDVIDSVAKKYREHDMPGGWILPNDGYGCGY 335

Query: 275 RVFTWNKGTFKNYKEMLKNLKSMGFKVVTIVDPGVKR 311
                      +  ++++ L   GF+     + GV +
Sbjct: 336 ----------TDLPKVVEGLAKYGFRTGLWTEDGVDK 362


Lambda     K      H
   0.320    0.141    0.426 

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: 2097
Number of extensions: 120
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 751
Length of database: 1108
Length adjustment: 43
Effective length of query: 708
Effective length of database: 1065
Effective search space:   754020
Effective search space used:   754020
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 (21.8 bits)
S2: 56 (26.2 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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