Align Na+/solute symporter (characterized, see rationale)
to candidate BPHYT_RS06030 BPHYT_RS06030 sodium:solute symporter
Query= uniprot:B2T7V3 (493 letters) >FitnessBrowser__BFirm:BPHYT_RS06030 Length = 516 Score = 533 bits (1374), Expect = e-156 Identities = 277/497 (55%), Positives = 352/497 (70%), Gaps = 24/497 (4%) Query: 7 VNPVAMTVFIAFFVLVTVIGFFAARWKRGDLTQLHEWGLGGRQFGTVISWFLVGGDFYTA 66 +N +A VF+ FF+ VT++GF AA W+RGDL L EWGLGGR+FGT+++WFL+GGD YTA Sbjct: 1 MNAIATFVFVLFFIGVTILGFIAAHWRRGDLAHLEEWGLGGRRFGTIVTWFLLGGDLYTA 60 Query: 67 YTVIAVPALVYSVGAYGFFALPYTIIVYPFVFAVMPKLWKIAHAKNHITAADYVQGEYGG 126 YT IAVPALV+ GA GFFALPYTI++YPF F V PKLW IA + ++T+AD+V YG Sbjct: 61 YTFIAVPALVFGAGATGFFALPYTILIYPFAFVVFPKLWSIAKRQGYVTSADFVSARYGS 120 Query: 127 KWFPAAVAITGIVATMPYIALQLVGMQVVIKGL-----GVTGEMPLIVAFVILALYTYAS 181 + A+A+TGIVATMPYIALQLVG++VVI L G G++PLI+AF ILA YTY S Sbjct: 121 RMLALAIAVTGIVATMPYIALQLVGIEVVIGALGFDTKGFVGDLPLIIAFAILAAYTYTS 180 Query: 182 GLRAPAMIAFVKDIMIYIVVIAAVWLIPAKLGGYAHVFDA---ADTYFKAKGGATGIILK 238 GLRAPAMIA VKD++IYI + AA+ +IP +LGG+ H+F A KA + Sbjct: 181 GLRAPAMIAVVKDVLIYITIFAAIIVIPPQLGGFGHIFSVVPPAKLLLKAPD-----VSS 235 Query: 239 PTQFTAYASLALGSALAAFMYPHTMTAVLSSSSANTVRKNAIFLPAYTLLLGLIALLGYM 298 ++AYA+LA+GSALA F+YPH++TAVLSS S NT+R+N LPAY+L+LGL+ALLG+M Sbjct: 236 LNGYSAYATLAVGSALALFLYPHSITAVLSSKSGNTIRRNMAMLPAYSLVLGLLALLGFM 295 Query: 299 AIAAGV----------HVKSASDMVPALFNTLFPSWFVGFAAAAIAISALVPAAIMSIGA 348 A+A+GV + VPALF FPSWFVG A AAI I ALVPAAIMSI A Sbjct: 296 ALASGVKDMPEFAPYFKAFGPNFAVPALFLHYFPSWFVGVAFAAIGIGALVPAAIMSIAA 355 Query: 349 ANLFTRNLWRPLVSPNISPEGEASTAKIVSLVVKFGALLFIVFLPTQYAIDLQLLGGVWI 408 ANL+TRN+ + V+ N++ E E + AK+VSL+VK GA+ FI+ LP YAI LQLLGG+WI Sbjct: 356 ANLYTRNIHKEFVNRNMTHEQETNVAKLVSLIVKVGAVAFILGLPLTYAIQLQLLGGIWI 415 Query: 409 LQIFPAIVFSLYTRRLNTPGLFLGWLAGIVLGTGLAISQGLK-PVFALHLGDAVYPVYIG 467 +Q PAIV LYTR L+ GL GW GI GT +AIS L +F +HL P Y Sbjct: 416 IQTLPAIVLGLYTRVLDYRGLLAGWAVGIATGTWMAISLKLAGSIFTIHLFGMAIPGYAA 475 Query: 468 LIALTVNIVVSFVVSVL 484 + +L VN+VV+ VVS+L Sbjct: 476 VWSLIVNLVVAVVVSLL 492 Lambda K H 0.328 0.141 0.431 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: 868 Number of extensions: 46 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: 493 Length of database: 516 Length adjustment: 34 Effective length of query: 459 Effective length of database: 482 Effective search space: 221238 Effective search space used: 221238 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 (21.8 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 17 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