Align Monocarboxylic acid transporter (characterized)
to candidate 7024383 Shewana3_1575 Na+/solute symporter (RefSeq)
Query= SwissProt::Q8NS49 (551 letters) >FitnessBrowser__ANA3:7024383 Length = 578 Score = 169 bits (427), Expect = 4e-46 Identities = 135/514 (26%), Positives = 221/514 (42%), Gaps = 86/514 (16%) Query: 27 VVFIIVTMTVVLRVG----KSTSESTDFYTGGASFSGTQNGLAIAGDYLSAASFLGIVGA 82 + ++IV ++ L +G + +FY G NG+A A D++SAASF+ + G Sbjct: 6 LTYLIVGLSFALYIGIAIWSRAGSTKEFYVAGGGVHPVVNGMATAADWMSAASFISLAGI 65 Query: 83 ISLNGYDGFLYSIGFFVAWLVALLLVAEPLRNVGRFTMADVLSFRLRQKPVRVAAACGTL 142 +S GYDG +Y +G+ +++ L +A LR G+FT+ D + R + R A + Sbjct: 66 VSFVGYDGSVYLMGWTGGYVLLALCMAPYLRKFGKFTVPDFVGERYYSQAARTVAVICAI 125 Query: 143 AVTLFYLIAQMAGAGSLVSVLLDIHEFKWQAVVVGIVGIVMIAYVLLGGMKGTTYVQMIK 202 + Y+ QM G G + S L++ V +G+ V+ Y +LGGMKG TY Q+ + Sbjct: 126 FICFTYIAGQMRGVGVVFSRFLEVDVD--TGVYIGMA--VVFFYAVLGGMKGITYTQVAQ 181 Query: 203 AVLLVGGVAIMTVLTFVKVSG------GLTTLLNDAVEKHAA-------SDYAATKGYDP 249 +L+ + + V ++G G L DA ++ ++ + G+ P Sbjct: 182 YCVLIFAFMVPAIFLSVMMTGHIIPQIGFGAQLLDAAGNNSGVYLLEKLNNLSVDLGFAP 241 Query: 250 TQILEPGLQYGATLTTQLDFISLALALCLGTAGLPHVLMRFYTVPTAKEARKSVTWAIVL 309 Y + +D + AL +GTAGLPHV++RF+TVP K+AR S WA+V Sbjct: 242 ---------YTDGSKSMIDVFCITGALMVGTAGLPHVIVRFFTVPKVKDARVSAGWALVF 292 Query: 310 IGAFYLMTLVLG----------------YGAAALVGPD--------------------RV 333 I Y L G A PD ++ Sbjct: 293 IAIMYTTVPALAAFSRVNMIETINGPDQKGVAYETAPDWIKNWEKTGLIKWDDKNGDGKI 352 Query: 334 IAAPGAANAAAPLLAFELGGSIF--------------MALISAVAFATVLAVVAGLAITA 379 A G AA ++ I +AL++A A L+ AGL + Sbjct: 353 YYAKGKMEDAASPNEMKIDNDIIVLATPEIANLPAWVIALVAAGGLAAALSTSAGLLLVI 412 Query: 380 SAAVGHDIYNAVIRNGQSTEAEQVRVSRITVVVIGLISIVLGILAMTQN--VAFLVALAF 437 S +V HD+ + S + E + + G+ ++ G + VA +VA AF Sbjct: 413 STSVSHDLLKKNLMPNISDKKELMYAR----LAAGIGIVIAGYFGVNPPGFVAAVVAFAF 468 Query: 438 AVAASANLPTILYSLYWKKFNTTGAVAAIYTGLI 471 +AAS+ P I+ ++ K N GA+A + GL+ Sbjct: 469 GLAASSLFPAIIMGIFSKTMNKEGAIAGMVIGLL 502 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: 640 Number of extensions: 30 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