Align Monocarboxylic acid transporter (characterized)
to candidate 201983 SO2857 sodium/solute symporter family protein (NCBI ptt file)
Query= SwissProt::Q8NS49 (551 letters) >FitnessBrowser__MR1:201983 Length = 578 Score = 171 bits (432), Expect = 9e-47 Identities = 154/589 (26%), Positives = 256/589 (43%), Gaps = 80/589 (13%) Query: 27 VVFIIVTMTVVLRVGKS----TSESTDFYTGGASFSGTQNGLAIAGDYLSAASFLGIVGA 82 + ++IV ++ L +G + + +FY G NG+A A D++SAASF+ + G Sbjct: 6 LTYLIVGLSFALYIGIALWTRAGSTKEFYVAGGGVHPVVNGMATAADWMSAASFISLAGI 65 Query: 83 ISLNGYDGFLYSIGFFVAWLVALLLVAEPLRNVGRFTMADVLSFRLRQKPVRVAAACGTL 142 +S GYDG +Y +G+ +++ L +A LR G+FT+ D L R + R A + Sbjct: 66 VSFVGYDGSVYLMGWTGGYVLLALCMAPYLRKFGKFTVPDFLGERYYSQAARTVAVICAI 125 Query: 143 AVTLFYLIAQMAGAGSLVSVLLDIHEFKWQAVVVGIVGIVMIAYVLLGGMKGTTYVQMIK 202 + Y+ QM G G + S L++ V +G+ V+ Y +LGGMKG TY Q+ + Sbjct: 126 FICFTYIAGQMRGVGVVFSRFLEVEVD--TGVYIGMA--VVFFYSVLGGMKGITYTQVAQ 181 Query: 203 AVLLVGGVAIMTVLTFVKVSGGLTTLLNDAVE-KHAASDYAATKGYDPTQILEPGL---Q 258 +L+ + + V ++G + + + AA + + D L L Sbjct: 182 YCVLIFAFMVPAIFLSVMMTGHIIPQIGFGAQLLDAAGNNSGVYLLDKLNNLSVDLGFAP 241 Query: 259 YGATLTTQLDFISLALALCLGTAGLPHVLMRFYTVPTAKEARKSVTWAIVLIGAFYLMTL 318 Y + +D + + AL +GTAGLPHV++RF+TVP K+AR S WA+V I Y T Sbjct: 242 YTDGSKSMIDVLCITGALMVGTAGLPHVIVRFFTVPKVKDARVSAGWALVFIAIMY--TT 299 Query: 319 VLGYGAAALV-------GPD-------------------------------RVIAAPGAA 340 V A + V GPD ++ A G Sbjct: 300 VPALAAFSRVNMIETINGPDQKGVAYETAPNWIKNWEKTGLIKWDDKNGDGKIYYATGKI 359 Query: 341 NAAAPLLAFELGGSIF--------------MALISAVAFATVLAVVAGLAITASAAVGHD 386 AA ++ I +AL++A A L+ AGL + S +V HD Sbjct: 360 EDAASTNEMKIDNDIIVLATPEIANLPAWVIALVAAGGLAAALSTSAGLLLVISTSVSHD 419 Query: 387 IYNAVIRNGQSTEAEQVRVSRITVVVIGLISIVLGILAMTQN--VAFLVALAFAVAASAN 444 + + S + E + + G+ ++ G + VA +VA AF +AAS+ Sbjct: 420 LLKKNLMPNISDKKELMYAR----LAAGIGIVIAGYFGVNPPGFVAAVVAFAFGLAASSL 475 Query: 445 LPTILYSLYWKKFNTTGAVAAIYTGLISALLLIFLSPAVSGNDSAMVPGADWAI-FPLKN 503 P I+ ++ K N GA+A + GL I + + +A VP A+W + + Sbjct: 476 FPAIIMGIFSKTMNKEGAIAGMILGLFFTSGYIVYFKFI--DPTANVP-ANWFLGISPEG 532 Query: 504 PGLVSIPLAFIAGWIGTLVGKPDNMDDLAAEMEVRSLT-GVGVEKAVDH 551 G+V + + F+ + +V K + + V S+ G +A DH Sbjct: 533 IGMVGMVINFV---VAAIVSKVTAATPVHVQEMVESIRFPKGAGEASDH 578 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: 643 Number of extensions: 32 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: 578 Length adjustment: 36 Effective length of query: 515 Effective length of database: 542 Effective search space: 279130 Effective search space used: 279130 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