GapMind for catabolism of small carbon sources

 

Alignments 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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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:

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:

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:

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:

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