Align Alpha-ketoglutarate permease of 435 aas and 12 TMSs (characterized)
to candidate BWI76_RS19335 BWI76_RS19335 MFS transporter
Query= TCDB::O05390 (435 letters) >FitnessBrowser__Koxy:BWI76_RS19335 Length = 425 Score = 323 bits (827), Expect = 8e-93 Identities = 150/400 (37%), Positives = 239/400 (59%), Gaps = 4/400 (1%) Query: 14 IGIPSHMVWGYIGVVIFMVGDGLEQGWLSPFLVDHGLSMQQSASLFTMYGIAVTISAWLS 73 +G+P +++WGYI + +FM GDG E +LS ++ + G S Q++ FT+YG+A +SAW+S Sbjct: 9 LGLPLNLLWGYIAIAVFMTGDGFELAFLSHYIKELGFSPAQASFAFTLYGLAAALSAWIS 68 Query: 74 GTFVQTWGPRKTMTVGLLAFILGSAAFIGWAIPHMYYPALLGSYALRGLGYPLFAYSFLV 133 G + P KTM +G + + + F+ + + H Y +L Y +RG YPLF YSF+V Sbjct: 69 GVVAEIITPLKTMMIGFVLWCVFHVLFLVFGLGHANYALILVFYGIRGFAYPLFLYSFIV 128 Query: 134 WVSYSTSQNILGKAVGWFWFMFTCGLNVLGPFYSSYAVPAFGEINTLWSALLFVAAGGIL 193 + ++ + A+GWFW +++ G+ V G + S+ +P GE+ TLW AL F GGI+ Sbjct: 129 AIIHNVKSDNASSAIGWFWAVYSIGIGVFGSYIPSFTIPHIGELGTLWLALAFCVTGGII 188 Query: 194 ALFFNKDKFTPIQKQD---QPKWKELSKAFTIMFENPKVGIGGVVKTINAIGQFGFAIFL 250 AL + TP Q+ + K+ EL +A T+++ N + + +V+ IN + FGFA+ + Sbjct: 189 ALASLRHIQTPRHMQNLTTREKFSELGRAATLLYTNRNILLSSMVRIINTLSLFGFAVIM 248 Query: 251 P-TYLARYGYSVSEWLQIWGTLFFVNIVFNIIFGAVGDKLGWRNTVMWFGGVGCGIFTLA 309 P ++ G++ SEWLQ+W FF I N+++G +G+KLGW V WFG +G + +LA Sbjct: 249 PMMFVDELGFTTSEWLQVWAVFFFTTIFSNVLWGILGEKLGWMKVVRWFGCIGMALSSLA 308 Query: 310 LYYTPQLIGHQYWVLMIIACCYGAALAGYVPLSALLPTLAPDNKGAAMSVLNLGSGLCAF 369 YY PQ GH + + MI A G +A +VPL+A+ P L P +KGAA+SV NL +G+ F Sbjct: 309 FYYIPQHFGHNFAMAMIPAIALGIFVAAFVPLAAVFPALEPKHKGAAISVYNLSAGMSNF 368 Query: 370 IAPGIVSLFIGPLGAGGVIWIFAALYFFSAFLTRFLTISE 409 +AP I + + GV+ + ALY + FL F+ + + Sbjct: 369 LAPAIAVILLPFFSTIGVVIAYTALYVAAFFLCAFIRVEQ 408 Lambda K H 0.327 0.143 0.467 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: 727 Number of extensions: 48 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: 435 Length of database: 425 Length adjustment: 32 Effective length of query: 403 Effective length of database: 393 Effective search space: 158379 Effective search space used: 158379 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: 51 (24.3 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