Align Myoinositol:Na+ symporter, SMIT1 (characterized)
to candidate WP_057509052.1 ABB28_RS13160 sodium transporter
Query= TCDB::P31637 (718 letters) >NCBI__GCF_001431535.1:WP_057509052.1 Length = 520 Score = 249 bits (636), Expect = 2e-70 Identities = 185/554 (33%), Positives = 283/554 (51%), Gaps = 81/554 (14%) Query: 5 LETADIAIVALYFILVMCIGFFAMWKSNRST-----VSGYFLAGRSMTWVAIGASLFVSN 59 L D +IV +Y V + A W S YFLA +S+ W A+GASL +N Sbjct: 3 LSVLDTSIVLVYLAGVFVL---AQWVSREKAGHAKDAKDYFLASKSLPWWAVGASLIAAN 59 Query: 60 IGSEHFIGLAGSGAASGFAVGAWEFNALLLLQLLGWVFIPIYIRSGVYTMPEYLSKRFGG 119 I +E IG++GSG A G A+ ++E+ A L L ++G F+P+++R+G+YTMP++L +R+ G Sbjct: 60 ISAEQIIGMSGSGYAIGLAIASYEWMAALTLLIVGKWFLPVFLRNGIYTMPQFLEQRY-G 118 Query: 120 HRIQVYFAALSLILYIFTKLSVDLYSGALFIQESLGWNLYVSVILLIGMTALLTVTGGLV 179 RI+ A L LY+F ++ L+ GA+ + + G + ++V+L+ L + GGL Sbjct: 119 TRIRTLMAVFWLGLYVFVNVTSILWLGAIAVSQVTGMDQMLAVVLIGVFALLYQLYGGLK 178 Query: 180 AVIYTDTLQALLMIVGALTLMIISMMEIG---GFEEVKRRYMLASPNVTSILLTYNLSNT 236 AV TD +Q L+++G L + +++ ++G G +R A P ++L+ Sbjct: 179 AVALTDIVQVSLLVLGGLLVTGLTLSQLGEGAGIVAGMQRLWEAHPGHFEMILS------ 232 Query: 237 NSCNVHPKKDALKMLRNPTDEDVPWPGFVLGQTPASVW-----YWCADQVIVQRVLAAKN 291 KD N +D+P ++G +W YW +Q I+QR LAAK+ Sbjct: 233 --------KD------NLFYKDLPGISVLVG----GLWIMNLSYWGFNQYIIQRALAAKD 274 Query: 292 IAHAKGSTLMAGFLKLLPMFIIVVPGMISRILFADDIACINPEHCMQVCGSRAGCSNIAY 351 I A+ L A FLKLL I+VVPG I+ ++ A + + AY Sbjct: 275 IGEAQKGVLFAAFLKLLMPLIVVVPG-IAAVMLAPGL----------------DAPDQAY 317 Query: 352 PRLVMKLVPVGLRGLMMAVMIAALMSDLDSIFNSASTIFTLDVYKLIRRSASSRELMIVG 411 P + M+L+P G+ G++ A ++AA+++ L S NS +TIFTLD Y + L+ VG Sbjct: 318 PTM-MRLLPTGILGMVFAALVAAIVASLASKINSVATIFTLDFYAQRKGPHDEATLVRVG 376 Query: 412 RIFVAFMVVISI-AWVPIIVEMQGGQMYLYIQEVADYLTPPVAALFLLAIFWKRCNEQGA 470 RI A VV+ I A P++ Q + YIQE + TP + +FLL +FWKR NE GA Sbjct: 377 RIAAAVTVVLGILAAKPLLGSFD--QAFQYIQEYTGFFTPGIVVIFLLGLFWKRANEAGA 434 Query: 471 FYGGMAGFVLGAVRLTLAFAYRAPECDQPDNRPGFIKDIHYMYVATALFWVTGLITVIVS 530 + FVL V L LA+ P D R G + F + L+ V VS Sbjct: 435 LAAAVGSFVLSVV-LKLAWP-SLPFID----RVGLV------------FLLALLLAVGVS 476 Query: 531 LLTP-PPTKEQIRT 543 L TP P K+ +RT Sbjct: 477 LATPAAPAKDVVRT 490 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: 936 Number of extensions: 40 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: 520 Length adjustment: 37 Effective length of query: 681 Effective length of database: 483 Effective search space: 328923 Effective search space used: 328923 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: 53 (25.0 bits)
This GapMind analysis is from Sep 24 2021. 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