GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMIT1 in Pedobacter sp. GW460-11-11-14-LB5

Align Myoinositol:Na+ symporter, SMIT1 (characterized)
to candidate CA265_RS04220 CA265_RS04220 sodium:solute symporter

Query= TCDB::P31637
         (718 letters)



>FitnessBrowser__Pedo557:CA265_RS04220
          Length = 550

 Score =  288 bits (738), Expect = 4e-82
 Identities = 173/551 (31%), Positives = 293/551 (53%), Gaps = 41/551 (7%)

Query: 4   VLETADIAIVALYFILVMCIGFFA--MWKSNRSTVSG-YFLAGRSMTWVAIGASLFVSNI 60
           ++ T DI I   Y + ++ IG +     K N  T SG YFLAG+++ W  IG +LF +NI
Sbjct: 1   MISTTDIVITIAYILFIVTIGLWTGTRKKKNEETTSGEYFLAGKTLKWPMIGLALFATNI 60

Query: 61  GSEHFIGLAGSGAASGFAVGAWEFNALLLLQLLGWVFIPIYIRSGVYTMPEYLSKRFGGH 120
              H + LA SG  SG   G +E+ A   L LL  +FIP YIRSG+ T+P++L +R+   
Sbjct: 61  SCLHLVSLAQSGFDSGLLNGNFEWMAAFTLILLALLFIPFYIRSGISTLPDFLERRY-NR 119

Query: 121 RIQVYFAALSLILYIFTKLSVDLYSGALFIQESLGWNLYVSVILLIGMTALLTVTGGLVA 180
             + + A +S++  I   ++    +G + ++   G ++YVS++++  +T L T+ GGL A
Sbjct: 120 ACRDWLAFISILSAIIIHIAFSFLAGGIVLETLFGIDMYVSIVVIALLTGLYTIIGGLRA 179

Query: 181 VIYTDTLQALLMIVGALTLMIISMMEIGGFEEVKRRYMLASPNVTSILLTYNLSNTNSCN 240
           V+ T+T+Q+L++I GA+ +   +  ++GG++           ++T+IL   N        
Sbjct: 180 VVVTETIQSLVLITGAIIITYFAWNKVGGWD-----------HMTAILQKEN-------- 220

Query: 241 VHPKKDALKMLRNPTDED-VPWPGFVLGQTPASVWYWCADQVIVQRVLAAKNIAHAKGST 299
                D L M+R   D+  + W    LG     +WYWCADQ IVQRVL AK+  HA+  +
Sbjct: 221 ---AMDKLSMIRPIGDKSGMSWIAVFLGYPVLGIWYWCADQTIVQRVLGAKDENHARVGS 277

Query: 300 LMAGFLKLLPMFIIVVPGMISRILFADDIACINPEHCMQVCGSRAGCSNIAYPRLVMKLV 359
           L  GF+K+LP+FI V+PG+ + IL+      ++    +   G     +   Y  ++ +L+
Sbjct: 278 LFCGFIKILPVFIFVLPGLFAYILYKSGTMDLSSLQTVGSNGETVLNTKGIYTLMITQLL 337

Query: 360 PVGLRGLMMAVMIAALMSDLDSIFNSASTIFTLDVYKLIRRSASSRELMIVGRIFVAFMV 419
           P GL G+++A +++ LMS +    NS +T+ + D+YK  +   S ++L+ VGR      +
Sbjct: 338 PKGLVGILVAALLSGLMSQIAGALNSIATLSSYDLYKRFKPETSDKKLVSVGRWSAGIAL 397

Query: 420 VISIAWVPIIVEMQGGQMYLYIQEVADYLTPPVAALFLLAIFWKRCNEQGAFYGGMAGFV 479
            +SI  +P++   +   ++  I +V  ++ PP+  +FLL +FWK+ + +GA Y  + G +
Sbjct: 398 TVSIGLLPLLNSYE--SLFNGINDVIAHIAPPITCVFLLGVFWKKASAKGAQYTLLLGSI 455

Query: 480 LGAVRLTLAFAYRAPECDQPDNRPGFIKDIHYMYVATALFWVTGLITVIVSLLTPPPTKE 539
           +GA    +   Y              I  I +M +A  LF +  LI V+ S + P     
Sbjct: 456 IGAGVFVVNKVY---------GTETIIGQIPFMMMAFYLFCICVLIQVVFSHIYPVKHTA 506

Query: 540 QIRT---TTFW 547
           Q  T   T+ W
Sbjct: 507 QSETLYWTSIW 517


Lambda     K      H
   0.325    0.139    0.422 

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: 989
Number of extensions: 57
Number of successful extensions: 5
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: 718
Length of database: 550
Length adjustment: 38
Effective length of query: 680
Effective length of database: 512
Effective search space:   348160
Effective search space used:   348160
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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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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