GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Pedo557:CA265_RS04220 CA265_RS04220
           sodium:solute symporter
          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 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