Align TRAP-type large permease component (characterized, see rationale)
to candidate Ac3H11_1228 TRAP-type C4-dicarboxylate transport system, large permease component
Query= uniprot:Q930R2 (425 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1228 Length = 426 Score = 552 bits (1423), Expect = e-162 Identities = 267/424 (62%), Positives = 348/424 (82%) Query: 1 MTLVVFIVSLLGAMAIGVPVAFSLMFCGVVLMWYMGMFNTQIIAQNMIAGADTFTLLAIP 60 MT+ +F+ SLL AMAIG+P+AF+L+ GV LMW++ +F+ QI+AQN+I GAD+F LLA+P Sbjct: 1 MTVTIFLGSLLLAMAIGIPIAFALLISGVALMWHLDLFDAQILAQNVINGADSFPLLAVP 60 Query: 61 FFILAGELMNAGGLSRRIIDFAIACVGHIRGGLGIVAIMAAVIMASISGSAAADTAALAA 120 FF+LAGE+MN GGLS+RI+ A+ VGH+ GGLG VAIMAAVI+A++SGSA AD AALA+ Sbjct: 61 FFMLAGEIMNVGGLSKRIVKLALTLVGHVPGGLGYVAIMAAVILAAVSGSAVADAAALAS 120 Query: 121 ILIPMMAKAGYNVPRSAGLIAAGGVIAPVIPPSMAFIVFGVAANVSITQLFMAGIVPGLI 180 +L+PMM AG+N RSAGLIA+ G+IAPVIPPS+ F++FGVAANVSI++LF+AGIVPG++ Sbjct: 121 LLLPMMVAAGHNKERSAGLIASAGIIAPVIPPSIGFVIFGVAANVSISKLFLAGIVPGIL 180 Query: 181 MGIALVATWLLVVRKDDIQPLPRTPMKERVGATGRALWALGMPVIILGGIKAGVVTPTEA 240 +G+AL TW +VR++D+ P R E A A+WALG+P+IIL G++ GV TPTEA Sbjct: 181 LGVALALTWWWLVRREDVAPPKRATRAELTVALREAVWALGLPIIILVGLRMGVFTPTEA 240 Query: 241 AVVAAVYALFVGMVIYRELKPRDLPGVILQAAKTTAVIMFLVCAALVSSWLITAANIPSE 300 AVVAAVYALFV MV+YREL L + +A+T+AV+MFLV AA+VS+WLIT A++PS+ Sbjct: 241 AVVAAVYALFVSMVVYRELSWHQLADIFRASARTSAVVMFLVAAAMVSAWLITVADLPSK 300 Query: 301 ITGFISPLIDRPTLLMFVIMLVVLVVGTALDLTPTILILTPVLMPIIKQAGIDPVYFGVL 360 + G + P + PTLL+ IML+V+VVGTA+D+TPTILILTPVLMP++K AGIDPVYFGVL Sbjct: 301 VIGMLEPFMGNPTLLLIAIMLLVMVVGTAMDMTPTILILTPVLMPVVKAAGIDPVYFGVL 360 Query: 361 FIMNTCIGLLTPPVGVVLNVVSGVGRVPLGKVIVGVTPFLVAQILVLFLLVLFPDIVIVP 420 FI+N IGL+TPPVG VLNVV+GVGR+ + +V GVTPF++AQ+ V+FLLVLFP IV+VP Sbjct: 361 FIINNAIGLITPPVGTVLNVVAGVGRMSMSQVTRGVTPFMLAQLAVMFLLVLFPSIVMVP 420 Query: 421 ARWL 424 RWL Sbjct: 421 LRWL 424 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: 566 Number of extensions: 19 Number of successful extensions: 1 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: 426 Length adjustment: 32 Effective length of query: 393 Effective length of database: 394 Effective search space: 154842 Effective search space used: 154842 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