Align Monocarboxylate transport permease protein (characterized)
to candidate WP_036262787.1 DL86_RS14170 sodium:solute symporter family protein
Query= SwissProt::Q1M7A2 (491 letters) >NCBI__GCF_000746085.1:WP_036262787.1 Length = 494 Score = 738 bits (1905), Expect = 0.0 Identities = 361/483 (74%), Positives = 415/483 (85%) Query: 1 MTTDINGTALAVFIFFFVLVTVMGFVASRWRKPETLAHIDEWGLGGRNFGTWITWFLVGG 60 MT + + ALAVFIFFF LVTV+GF+A+ WR+P+TLAH+DEWGLGGR FGTWITWFL+GG Sbjct: 1 MTGEFDYPALAVFIFFFALVTVLGFIAAHWRRPKTLAHLDEWGLGGRQFGTWITWFLIGG 60 Query: 61 DFYTAYTVIAVPALVYTVGAYGFFALPYTIVVYPFVFMVMPVLWKRAKDFGYVTAGDVVH 120 D YTAYT+IAVPALVY VGA+GFFA+PYTI++YPFVF VMP+LWK AK+ YVTA DVVH Sbjct: 61 DIYTAYTMIAVPALVYAVGAFGFFAMPYTIIIYPFVFAVMPILWKVAKENNYVTAADVVH 120 Query: 121 GQYGSRGLELAVAATGVIATMPYIALQLVGMTAVLKALGLHGELPLAIAFIVLALYTYSA 180 G+YGSR LELAVA TGVIATMPYIALQL+GM ++ ALGL GE+PL +AF++LA YTYS+ Sbjct: 121 GRYGSRPLELAVALTGVIATMPYIALQLIGMETIIHALGLKGEIPLILAFLILAFYTYSS 180 Query: 181 GLRAPALIAFVKDIMIYIVVIAAVALIPSKLGGYANVFASADAAFQAKGSGNLLLGGNQY 240 GLRAPALIAFVKD MIYIVVIAA ALIP KLGGY VF +ADAAF+AKGSG +LL +QY Sbjct: 181 GLRAPALIAFVKDTMIYIVVIAATALIPLKLGGYGAVFDAADAAFKAKGSGGILLAPSQY 240 Query: 241 VAYATLALGSALAAFMYPHTLTGIFASNSGKTIRKNAIMLPAYTLLLGLLALLGYMGHAA 300 V Y TLA GSALA FMYPH LT IFAS+ KTIR+NA++LP Y+L+LGLLAL+GYMGHAA Sbjct: 241 VPYLTLAFGSALALFMYPHALTAIFASSGAKTIRRNAMLLPTYSLVLGLLALMGYMGHAA 300 Query: 301 NLKLDSANDVVPTLFKTLFSGWFSGFAFAAIAIGALVPAAVMSIGAANLFTRNFWKAYVD 360 L L + NDVVP LFKTLF GWF+GFAFAAIAIGALVPAAVMSIGAANLFTRNFWKAYVD Sbjct: 301 GLTLSNNNDVVPALFKTLFPGWFAGFAFAAIAIGALVPAAVMSIGAANLFTRNFWKAYVD 360 Query: 361 PDVSDAGEAKVAKITSLVVKVGALLVIIFLPTQFALDLQLLGGIWILQTLPALVFGLYTN 420 P V+ AGEA+VAK SLVVKVGALLVI+FLPTQFA+DLQLLGG+WILQT P+++FGLYT Sbjct: 361 PGVTPAGEAQVAKTASLVVKVGALLVILFLPTQFAIDLQLLGGLWILQTFPSVIFGLYTG 420 Query: 421 WFRAPGLLAGWFVGFGGGTFLVWDAGWKPLHLISLGGEPFTVYTGLLALAANIAVAVVVN 480 WFRA GLLAGW +GF GGT+LVW +KPLH ++ G VY+GLLALAANI VA +V+ Sbjct: 421 WFRASGLLAGWAIGFFGGTWLVWLNNYKPLHTLAFGETRVAVYSGLLALAANILVASLVS 480 Query: 481 ALL 483 A L Sbjct: 481 AAL 483 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: 903 Number of extensions: 54 Number of successful extensions: 2 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: 494 Length adjustment: 34 Effective length of query: 457 Effective length of database: 460 Effective search space: 210220 Effective search space used: 210220 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