Aligments for a candidate for susB in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Aligments for a candidate for susB in Klebsiella michiganensis M5al

Align alpha-glucosidase (EC 3.2.1.20) (characterized)
to candidate BWI76_RS06250 BWI76_RS06250 alpha-glycosidase

Query= BRENDA::P21517
         (604 letters)



>FitnessBrowser__Koxy:BWI76_RS06250
          Length = 605

 Score = 1040 bits (2690), Expect = 0.0
 Identities = 476/604 (78%), Positives = 534/604 (88%)

Query: 1   MLNAWHLPVPPFVKQSKDQLLITLWLTGEDPPQRIMLRTEHDNEEMSVPMHKQRSQPQPG 60
           ML AWHLPV PF+K+ +++L+ITLWL+G+D P R+ LR E DNEE+S+PMH+ R  P PG
Sbjct: 1   MLKAWHLPVAPFIKEQQERLMITLWLSGDDLPPRVTLRAEEDNEELSLPMHRLRQAPHPG 60

Query: 61  VTAWRAAIDLSSGQPRRRYSFKLLWHDRQRWFTPQGFSRMPPARLEQFAVDVPDIGPQWA 120
           V AWR  I+L +GQPRRRYSFKLLW DRQ WFTPQGF+R PPARLEQFAVD+PD GPQW 
Sbjct: 61  VVAWRGEINLVNGQPRRRYSFKLLWADRQLWFTPQGFNRFPPARLEQFAVDLPDSGPQWV 120

Query: 121 ADQIFYQIFPDRFARSLPREAEQDHVYYHHAAGQEIILRDWDEPVTAQAGGSTFYGGDLD 180
           ADQ+FYQIFPDRFARS  REAEQD  YYHHAAG +I+ + WDEP+TA+AGGSTFYGGDLD
Sbjct: 121 ADQVFYQIFPDRFARSQSREAEQDATYYHHAAGHDIVRKAWDEPLTAEAGGSTFYGGDLD 180

Query: 181 GISEKLPYLKKLGVTALYLNPVFKAPSVHKYDTEDYRHVDPQFGGDGALLRLRHNTQQLG 240
           GISEKLPYLK+LGVTALYLNPVF APSVHKYDTEDYR VDPQFGGD ALLRLRHNTQ+ G
Sbjct: 181 GISEKLPYLKQLGVTALYLNPVFVAPSVHKYDTEDYRRVDPQFGGDAALLRLRHNTQKEG 240

Query: 241 MRLVLDGVFNHSGDSHAWFDRHNRGTGGACHNPESPWRDWYSFSDDGTALDWLGYASLPK 300
           MRL+LDGVFNHSGDSHAWFDRH RG+GGACHN +SPWRDWY+FS +G A DWLGYASLPK
Sbjct: 241 MRLILDGVFNHSGDSHAWFDRHQRGSGGACHNADSPWRDWYNFSPEGVAHDWLGYASLPK 300

Query: 301 LDYQSESLVNEIYRGEDSIVRHWLKAPWNMDGWRLDVVHMLGEAGGARNNMQHVAGITEA 360
           LDY+S +L++EIY GEDS+VRHWLKAPW+MDGWRLDVVHMLGE GGARNN++H+AGIT+A
Sbjct: 301 LDYRSSTLIDEIYGGEDSVVRHWLKAPWSMDGWRLDVVHMLGEGGGARNNLRHIAGITQA 360

Query: 361 AKETQPEAYIVGEHFGDARQWLQADVEDAAMNYRGFTFPLWGFLANTDISYDPQQIDAQT 420
           AK  +P+A++ GEHFGDARQWLQADVED+AMNYRGFTFPLWGFLANTDISYDPQ+IDAQT
Sbjct: 361 AKLERPDAFVFGEHFGDARQWLQADVEDSAMNYRGFTFPLWGFLANTDISYDPQKIDAQT 420

Query: 421 CMAWMDNYRAGLSHQQQLRMFNQLDSHDTARFKTLLGRDIARLPLAVVWLFTWPGVPCIY 480
           CMAWMDNYRAGLSHQQQLRMFNQLDSHDTARFK+LLG+D+ARLPLAVVWLF+WPGVPCIY
Sbjct: 421 CMAWMDNYRAGLSHQQQLRMFNQLDSHDTARFKSLLGKDVARLPLAVVWLFSWPGVPCIY 480

Query: 481 YGDEVGLDGKNDPFCRKPFPWQVEKQDTALFALYQRMIALRKKSQALRHGGCQVLYAEDN 540
           YGDEVG+DG NDPFCRKPFPW    QD  L  LY+RM  LRK  QALR+GGCQV+YAEDN
Sbjct: 481 YGDEVGVDGNNDPFCRKPFPWDPALQDGDLLDLYKRMSKLRKAHQALRYGGCQVIYAEDN 540

Query: 541 VVVFVRVLNQQRVLVAINRGEACEVVLPASPFLNAVQWQCKEGHGQLTDGILALPAISAT 600
           VVVFVRV  QQRVLVAINRGEACEVV+  SP L+   WQ KEG G L DG+L LPAISA+
Sbjct: 541 VVVFVRVYKQQRVLVAINRGEACEVVIEDSPLLDVNGWQLKEGAGALHDGVLTLPAISAS 600

Query: 601 VWMN 604
           VW +
Sbjct: 601 VWFS 604


Lambda     K      H
   0.322    0.138    0.451 

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: 1571
Number of extensions: 62
Number of successful extensions: 1
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: 604
Length of database: 605
Length adjustment: 37
Effective length of query: 567
Effective length of database: 568
Effective search space:   322056
Effective search space used:   322056
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 (21.9 bits)
S2: 53 (25.0 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)
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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, or view the source code.

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