GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nupG in Klebsiella michiganensis M5al

Align Xanthosine permease; Xanthosine transporter (characterized)
to candidate BWI76_RS20600 BWI76_RS20600 nucleoside permease

Query= SwissProt::P45562
         (418 letters)



>FitnessBrowser__Koxy:BWI76_RS20600
          Length = 418

 Score =  724 bits (1870), Expect = 0.0
 Identities = 354/418 (84%), Positives = 387/418 (92%)

Query: 1   MSIAMRLKVMSFLQYFIWGSWLVTLGSYMINTLHFTGANVGMVYSSKGIAAIIMPGIMGI 60
           M IA RLK+MSFLQYFIWGSWLVTLGSYMINTLHFTGANVGMVYSSKG+AAIIMPG+MGI
Sbjct: 1   MGIASRLKLMSFLQYFIWGSWLVTLGSYMINTLHFTGANVGMVYSSKGLAAIIMPGVMGI 60

Query: 61  IADKWLRAERAYMLCHLVCAGVLFYAASVTDPDMMFWVMLVNAMAFMPTIALSNSVSYSC 120
           IADKWLRAERAYMLCHLVCAGVL YA +VTDPD MFWVML+NAMA+MPTI+LSNSVSYSC
Sbjct: 61  IADKWLRAERAYMLCHLVCAGVLLYATTVTDPDTMFWVMLINAMAYMPTISLSNSVSYSC 120

Query: 121 LAQAGLDPVTAFPPIRVFGTVGFIVAMWAVSLLHLELSSLQLYIASGASLLLSAYALTLP 180
           LAQ+G DP TAFPP+RVFGT+GFIVAMW VSL+ LELSS QLYIAS ASLLL+ YA TLP
Sbjct: 121 LAQSGQDPATAFPPVRVFGTLGFIVAMWMVSLMGLELSSAQLYIASAASLLLALYAFTLP 180

Query: 181 KIPVAEKKATTSLASKLGLDAFVLFKNPRMAIFFLFAMMLGAVLQITNVFGNPFLHDFAR 240
           KIPV EKKA+T+LA++LGLDAFVLFKNPRMAIFF FAMMLGAVLQITNVFGNPFLHDFAR
Sbjct: 181 KIPVTEKKASTTLAARLGLDAFVLFKNPRMAIFFFFAMMLGAVLQITNVFGNPFLHDFAR 240

Query: 241 NPEFADSFVVKYPSILLSVSQMAEVGFILTIPFFLKRFGIKTVMLMSMVAWTLRFGFFAY 300
           NP FADSFVV+YPSILLSVSQMAEV FILTIPFFLKRFGIKTVMLMSM+AWTLRFGFFA+
Sbjct: 241 NPAFADSFVVRYPSILLSVSQMAEVAFILTIPFFLKRFGIKTVMLMSMLAWTLRFGFFAF 300

Query: 301 GDPSTTGFILLLLSMIVYGCAFDFFNISGSVFVEQEVDSSIRASAQGLFMTMVNGVGAWV 360
           GDPS  GF+LLL+SMIVYGCAFDFFNISGSVFVEQ+V ++IRASAQGLFMTMVNGVGAWV
Sbjct: 301 GDPSPFGFVLLLMSMIVYGCAFDFFNISGSVFVEQQVGANIRASAQGLFMTMVNGVGAWV 360

Query: 361 GSILSGMAVDYFSVDGVKDWQTIWLVFAGYALFLAVIFFFGFKYNHDPEKIKHRAVTH 418
           GS+LSG+AVDYFS+DGVKDWQTIWLVFA Y+L LAVIF   F+Y H+PE+   + + H
Sbjct: 361 GSVLSGLAVDYFSLDGVKDWQTIWLVFAAYSLMLAVIFALFFRYKHEPEQRMEKELAH 418


Lambda     K      H
   0.330    0.141    0.435 

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: 699
Number of extensions: 20
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: 418
Length of database: 418
Length adjustment: 32
Effective length of query: 386
Effective length of database: 386
Effective search space:   148996
Effective search space used:   148996
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 50 (23.9 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