Align Monocarboxylate transport permease protein (characterized)
to candidate YP_002824475.1 NGR_b22770 monocarboxylic acid permease
Query= SwissProt::Q1M7A2 (491 letters) >NCBI__GCF_000018545.1:YP_002824475.1 Length = 502 Score = 767 bits (1980), Expect = 0.0 Identities = 378/486 (77%), Positives = 428/486 (88%) Query: 1 MTTDINGTALAVFIFFFVLVTVMGFVASRWRKPETLAHIDEWGLGGRNFGTWITWFLVGG 60 MT +I+ +ALAVFIFFFVLVT MGF ASRWR+ E+L H+DEWGLGGR FGTWITWFLVGG Sbjct: 1 MTANIDMSALAVFIFFFVLVTAMGFFASRWRRAESLDHLDEWGLGGRKFGTWITWFLVGG 60 Query: 61 DFYTAYTVIAVPALVYTVGAYGFFALPYTIVVYPFVFMVMPVLWKRAKDFGYVTAGDVVH 120 DFYTAYTVIAVPALVY +GAYGFFALPYTI+VYP VF VMP+LWK AK+ GYVTAGDVV Sbjct: 61 DFYTAYTVIAVPALVYAIGAYGFFALPYTIIVYPLVFAVMPLLWKAAKERGYVTAGDVVR 120 Query: 121 GQYGSRGLELAVAATGVIATMPYIALQLVGMTAVLKALGLHGELPLAIAFIVLALYTYSA 180 G YGSR LELAVA+TGVIATMPYIALQL+GM +KALGL GE+P+ +AF+VLALYTYS+ Sbjct: 121 GTYGSRALELAVASTGVIATMPYIALQLIGMEVAIKALGLTGEMPIVLAFLVLALYTYSS 180 Query: 181 GLRAPALIAFVKDIMIYIVVIAAVALIPSKLGGYANVFASADAAFQAKGSGNLLLGGNQY 240 GLRAPALIAFVKDIMIYIVV+AA+ ++PSKLGGY+ VF++ADAAF+AKG G +LL Q Sbjct: 181 GLRAPALIAFVKDIMIYIVVLAAIIVVPSKLGGYSAVFSAADAAFEAKGKGGILLDPAQL 240 Query: 241 VAYATLALGSALAAFMYPHTLTGIFASNSGKTIRKNAIMLPAYTLLLGLLALLGYMGHAA 300 V Y TLALGSALAAFMYPHTLTGIFAS+ TIRKNA++LPAYTLLLGLLALLGYMGHAA Sbjct: 241 VPYVTLALGSALAAFMYPHTLTGIFASSGANTIRKNAVLLPAYTLLLGLLALLGYMGHAA 300 Query: 301 NLKLDSANDVVPTLFKTLFSGWFSGFAFAAIAIGALVPAAVMSIGAANLFTRNFWKAYVD 360 L+L S NDVVPTLFKTLF GWF+GFAF+AIAIGALVPAAVMSIGAANLFTRNFWK +V+ Sbjct: 301 GLQLQSNNDVVPTLFKTLFPGWFAGFAFSAIAIGALVPAAVMSIGAANLFTRNFWKVWVN 360 Query: 361 PDVSDAGEAKVAKITSLVVKVGALLVIIFLPTQFALDLQLLGGIWILQTLPALVFGLYTN 420 PDV+ AGEA+VAKITS++VKVGAL+ I+ LPTQFALDLQLLGG+WILQTLPALVFGLYT+ Sbjct: 361 PDVTAAGEAQVAKITSMLVKVGALVAILLLPTQFALDLQLLGGLWILQTLPALVFGLYTS 420 Query: 421 WFRAPGLLAGWFVGFGGGTFLVWDAGWKPLHLISLGGEPFTVYTGLLALAANIAVAVVVN 480 WFRAP LLAGW GF GG+ LVW G KPLH ++ G +VYTGLLALA N+ VAVVVN Sbjct: 421 WFRAPALLAGWAAGFIGGSALVWSDGLKPLHALAFDGVTVSVYTGLLALALNVTVAVVVN 480 Query: 481 ALLPAK 486 ++PAK Sbjct: 481 LVVPAK 486 Lambda K H 0.327 0.142 0.439 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: 911 Number of extensions: 45 Number of successful extensions: 3 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: 491 Length of database: 502 Length adjustment: 34 Effective length of query: 457 Effective length of database: 468 Effective search space: 213876 Effective search space used: 213876 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 (21.7 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