Align Monocarboxylic acid transporter (characterized)
to candidate 5209923 Shew_2371 Na+/solute symporter (RefSeq)
Query= SwissProt::Q8NS49 (551 letters) >FitnessBrowser__PV4:5209923 Length = 572 Score = 177 bits (449), Expect = 1e-48 Identities = 159/586 (27%), Positives = 259/586 (44%), Gaps = 80/586 (13%) Query: 27 VVFIIVTMTVVLRVG----KSTSESTDFYTGGASFSGTQNGLAIAGDYLSAASFLGIVGA 82 + ++IV T L +G + +FY G NG+A A D++SAASF+ + G Sbjct: 6 LTYLIVGFTFALYIGIAIWSRAGSTKEFYVAGGGVHPVMNGMATAADWMSAASFISLAGI 65 Query: 83 ISLNGYDGFLYSIGFFVAWLVALLLVAEPLRNVGRFTMADVLSFRLRQKPVRVAAACGTL 142 +S GYDG +Y +G+ +++ L +A LR G+FT+ D + R + R A + Sbjct: 66 VSFVGYDGSVYLMGWTGGYVLLALCMAPYLRKFGKFTVPDFIGDRYYSQAARTVAVVCAI 125 Query: 143 AVTLFYLIAQMAGAGSLVSVLLDIHEFKWQAVVVGIVGIVMIAYVLLGGMKGTTYVQMIK 202 + Y+ QM G G + S L++ V +G+ V+ Y +LGGMKG TY Q+ + Sbjct: 126 FICFTYIAGQMRGVGVVFSRFLEVEVD--TGVYIGMA--VVFFYAVLGGMKGITYTQVAQ 181 Query: 203 AVLLVGGVAIMTVLTFVKVSGGLTTLLNDAVE-KHAASDYAATKGYDPTQILEPGL---Q 258 +L+ + + V ++G + L E AA + + L L Q Sbjct: 182 YCVLIFAFMVPAIFISVMMTGHILPQLGFGAELVDAAGNNTGVYLLEKLDGLSAQLGFSQ 241 Query: 259 YGATLTTQLDFISLALALCLGTAGLPHVLMRFYTVPTAKEARKSVTWAIVLIGAFYLMTL 318 Y +D + AL GTAGLPHV++RF+TVP K+AR S WA+V I Y T Sbjct: 242 YTEGSKGMIDVFFITGALMFGTAGLPHVIVRFFTVPKVKDARVSAGWALVFIAIMY--TT 299 Query: 319 VLGYGAAALVGPDRVIAAP---GAANAAAP--LLAFELGGSI------------------ 355 + A + V I P G A AP + +E G I Sbjct: 300 IPALAAFSRVNMIETINGPESTGVAYETAPDWIKNWEKTGLIKWDDKNNDGKIYYAKGET 359 Query: 356 -----------------------FMALISAVAFATVLAVVAGLAITASAAVGHDIYNAVI 392 +AL++A A L+ AGL + S +V HD+ Sbjct: 360 NEMKIDRDIMVLATPEIANLPAWVIALVAAGGLAAALSTSAGLLLVISTSVSHDLLKKNF 419 Query: 393 RNGQSTEAEQVRVSRITVVVIGLISIVLGILAMTQNVAFLVALAFAVAASANLPTILYSL 452 S + +++ +RI +G++ + VA +VA+AF +AAS+ P I+ + Sbjct: 420 MPDIS-DKQELLYARI-AAALGIVMAGYFGINPPGFVAAVVAIAFGLAASSLFPAIIMGI 477 Query: 453 YWKKFNTTGAVAAIYTGLI-SALLLIFLSPAVSGNDSAMVPGADWAIFPLKNPG------ 505 + + N GA+A + GL+ SA +I+ G+++A ++W +F + G Sbjct: 478 FSRTMNKEGAIAGMVIGLLFSASYIIYFKFVNPGDNNA----SNW-LFGISPEGIGMLGM 532 Query: 506 LVSIPLAFIAGWIGTLVGKPDNMDDLAAEMEVRSLTGVGVEKAVDH 551 +++ +AFI + V P N+ D+ +R G G +A DH Sbjct: 533 IINFAVAFIVSKVTAAV--PQNVVDMVE--SIRFPKGAG--EAHDH 572 Lambda K H 0.324 0.138 0.393 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: 634 Number of extensions: 31 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 551 Length of database: 572 Length adjustment: 36 Effective length of query: 515 Effective length of database: 536 Effective search space: 276040 Effective search space used: 276040 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 (21.5 bits) S2: 53 (25.0 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