Align Monocarboxylic acid transporter (characterized)
to candidate WP_075619342.1 GY23_RS11345 sodium/solute symporter
Query= SwissProt::Q8NS49 (551 letters) >NCBI__GCF_001939075.1:WP_075619342.1 Length = 511 Score = 481 bits (1238), Expect = e-140 Identities = 256/527 (48%), Positives = 366/527 (69%), Gaps = 24/527 (4%) Query: 18 NPILNISVFVVFIIVTMTVVLRVGKSTSESTDFYTGGASFSGTQNGLAIAGDYLSAASFL 77 NP++ I +F++ + +T+ + K T+ +++FYT G SG QNGLAI+GDYLSAASFL Sbjct: 2 NPVV-IILFLIIVGMTLAITYFAAKKTNTASEFYTAGGGLSGWQNGLAISGDYLSAASFL 60 Query: 78 GIVGAISLNGYDGFLYSIGFFVAWLVALLLVAEPLRNVGRFTMADVLSFRLRQKPVRVAA 137 GI GAI+L G+DGFL+SIG+ VA+LV L +VAEPLRN+G++T+AD+++ R K VR A Sbjct: 61 GIAGAIALYGFDGFLFSIGYLVAYLVVLFIVAEPLRNLGKYTLADMINSRFNAKKVRAGA 120 Query: 138 ACGTLAVTLFYLIAQMAGAGSLVSVLLDIHEFKWQAVVVGIVGIVMIAYVLLGGMKGTTY 197 A ++ + +FY+IAQ+ GAG+L+ +L DI W AV+ +VGI+M YVL GGM T++ Sbjct: 121 ALSSITIVIFYMIAQLVGAGALIQLLFDIPY--WVAVL--LVGIMMTIYVLFGGMTATSW 176 Query: 198 VQMIKAVLLVGGVAIMTVLTFVKVSGGLTTLLNDAVEKHAASDYAATKGYDPTQILEPGL 257 VQ+IKAVLL+ G I++ L K + + +E A G D L PG+ Sbjct: 177 VQIIKAVLLMAGTMIISFLVLAKFNFNI-------MEMFTFMKTATPHGAD---YLNPGV 226 Query: 258 QYGATLTTQLDFISLALALCLGTAGLPHVLMRFYTVPTAKEARKSVTWAIVLIGAFYLMT 317 +Y LD +SL +AL LGTAGLPH+LMRF+TV AK AR SV WA ++G FY+MT Sbjct: 227 KY----KVPLDTLSLMIALVLGTAGLPHILMRFFTVRDAKTARSSVMWATWIVGIFYVMT 282 Query: 318 LVLGYGAAALVGPDRVIAAPGAANAAAPLLAFELGGSIFMALISAVAFATVLAVVAGLAI 377 + LG+GAAA VG D +++ A N AAPLLA LGG + M+ +SAVAFAT+LAVVAGL + Sbjct: 283 IFLGFGAAAFVGQDLIVSTNPAGNMAAPLLAQALGGDLLMSFVSAVAFATILAVVAGLVL 342 Query: 378 TASAAVGHDIYNAVIRNGQSTEAEQVRVSRITVVVIGLISIVLGILAMTQNVAFLVALAF 437 + ++A HDIY +I+ G++TE +Q+ +R V + + SI+L + A + NVAFLV+LAF Sbjct: 343 SGASAFAHDIYGQIIKKGKATEKQQMNAARYASVGVAVFSIILALGAQSLNVAFLVSLAF 402 Query: 438 AVAASANLPTILYSLYWKKFNTTGAVAAIYTGLISALLLIFLSPAVSG--NDSAMVPGAD 495 +AASANLP I+Y+++WKKFNT GA++++ TGL+SAL+L+ +SP+V +A++ G Sbjct: 403 CIAASANLPVIVYTIFWKKFNTAGALSSMITGLVSALILVSISPSVMNPVEGAALITGN- 461 Query: 496 WAIFPLKNPGLVSIPLAFIAGWIGTLVGKPDNMDDLAAEMEVRSLTG 542 IFPL NP L+S+PL F+ GWIGT++ K N + AE++V++ TG Sbjct: 462 -PIFPLTNPALLSVPLGFLGGWIGTMLTKEVN-EAKFAEVKVKANTG 506 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: 654 Number of extensions: 34 Number of successful extensions: 4 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: 551 Length of database: 511 Length adjustment: 35 Effective length of query: 516 Effective length of database: 476 Effective search space: 245616 Effective search space used: 245616 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: 52 (24.6 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