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 Apr 09 2024. The underlying query database was built on Sep 17 2021.
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:
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