Align TRAP-type large permease component (characterized, see rationale)
to candidate RR42_RS06530 RR42_RS06530 C4-dicarboxylate ABC transporter
Query= uniprot:Q930R2 (425 letters) >FitnessBrowser__Cup4G11:RR42_RS06530 Length = 434 Score = 259 bits (663), Expect = 9e-74 Identities = 158/435 (36%), Positives = 245/435 (56%), Gaps = 18/435 (4%) Query: 1 MTLVVFI--VSLLGAMAIGVPVAFSLMFCGVVLMWYMG----MFNTQIIAQNMIAGADTF 54 MTL+ I V LG M +GVP+ SL G+V + MF + QN AG + Sbjct: 1 MTLIAIILFVVFLGLMMLGVPIGVSLGLGGLVAIGLSNLDTQMFGLLAVPQNFYAGLGKY 60 Query: 55 TLLAIPFFILAGELMNAGGLSRRIIDFAIACVGHIRGGLGIVAIMAAVIMASISGSAAAD 114 LLAIP F+L G + + G+++R++ FAIA VG G L +VAI+ A+ + ISGS A+ Sbjct: 61 PLLAIPMFVLVGSIFDRSGVAQRLVTFAIAIVGRGPGMLPLVAILVAMFLGGISGSGPAN 120 Query: 115 TAALAAILIPMMAKAGYNVPRSAGLIAAGGVIAPVIPPSMAFIVFGV-AANVSITQLFMA 173 AA+ ++I M++AGY SA ++ A +IPPS+AFI++ V S+ LF A Sbjct: 121 AAAVGGVMIAAMSRAGYPGAYSAAVVGAAAATDILIPPSVAFIIYSVLVPGASVPALFAA 180 Query: 174 GIVPGLIMGIALVATWLLVVRKDDI----QPLPRTPMKERVGATGRALWALGMPVIILGG 229 G++PG++ G+AL+ + + RK ++ LPR P + + A W L P +ILGG Sbjct: 181 GMIPGILAGVALIVPAVWLARKHNMGAIEAGLPRPPFWK---SLREAAWGLVAPFLILGG 237 Query: 230 IKAGVVTPTEAAVVAAVYALFVGMVIYRELKPRDLPGVILQAAKTTAVIMFLVCAALVSS 289 ++AG TPTEAAVVA VY LFVGMVIYR + RDL + +AA+T+AVI+ +V A + + Sbjct: 238 MRAGWFTPTEAAVVAVVYGLFVGMVIYRSISMRDLFVIFQEAAETSAVILLVVALAGIFA 297 Query: 290 WLITAANIPSEITGFISPLIDRPTLLMFVIMLVVLVVGTALDLTPTILILTPVLMPIIKQ 349 + ++ + + I+ ++ +I+ +++ VG LD LI P+L+PI Sbjct: 298 YALSTLGVIDPLANAIAHSGLGEYGVLALIVALLMTVGMFLDGISIFLIFVPLLLPIANA 357 Query: 350 AGIDPVYFGVLFIMNTCIGLLTPPVGVVLNVVSGVGRVPLGKVIVGVTPFLVAQILVLFL 409 +PV+FGV+ + +G TPP+ V L V + RV + + + V L+A + + L Sbjct: 358 FHWNPVWFGVVLTLKVALGQFTPPLAVNLMVSCRIARVRMEETVPWVVWMLLAMFVAMLL 417 Query: 410 LVLFPDIVIVPARWL 424 ++ FP + A WL Sbjct: 418 VLAFPPL----ATWL 428 Lambda K H 0.331 0.145 0.430 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: 585 Number of extensions: 39 Number of successful extensions: 5 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: 425 Length of database: 434 Length adjustment: 32 Effective length of query: 393 Effective length of database: 402 Effective search space: 157986 Effective search space used: 157986 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 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