Align TRAP-type large permease component (characterized, see rationale)
to candidate Ac3H11_3955 TRAP-type C4-dicarboxylate transport system, large permease component
Query= uniprot:Q930R2 (425 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3955 Length = 427 Score = 319 bits (817), Expect = 1e-91 Identities = 171/418 (40%), Positives = 264/418 (63%), Gaps = 3/418 (0%) Query: 1 MTLVVFIVSLLGAMAIGVPVAFSLMFCGVVLMWYMGMFNTQIIAQNMIAGADTFTLLAIP 60 M +V + + M IGVP+A+SL + ++ + ++ Q + +G + F+LLAIP Sbjct: 1 MDTLVLLGTFFVLMMIGVPIAYSLGLSALAGALWIDLPLDAVMIQ-VASGVNKFSLLAIP 59 Query: 61 FFILAGELMNAGGLSRRIIDFAIACVGHIRGGLGIVAIMAAVIMASISGSAAADTAALAA 120 FF+LAG +M GG++RR++ FA VG IRGGL +V I+A+ +ISGS+ ADTA++ + Sbjct: 60 FFVLAGAIMAEGGMARRLVAFAGVLVGFIRGGLSLVNILASTFFGAISGSSVADTASIGS 119 Query: 121 ILIPMMAKAGYNVPRSAGLIAAGGVIAPVIPPSMAFIVFGVAAN--VSITQLFMAGIVPG 178 +LIP M K GY P + + +G V A +IPPS +++ +AA VSI LFMAG++PG Sbjct: 120 VLIPEMEKKGYPRPFATAVTVSGSVQAILIPPSHNAVLYSLAAGGTVSIAALFMAGVLPG 179 Query: 179 LIMGIALVATWLLVVRKDDIQPLPRTPMKERVGATGRALWALGMPVIILGGIKAGVVTPT 238 L+MG+ L A L ++ P+K+ + ALW L VIILGGI +GV T Sbjct: 180 LLMGLTLAALCLFTAHREGYPKGEVIPLKQALKICVEALWGLMTMVIILGGILSGVFTAN 239 Query: 239 EAAVVAAVYALFVGMVIYRELKPRDLPGVILQAAKTTAVIMFLVCAALVSSWLITAANIP 298 E+A +A V+A FV M IYR+ K RDLP ++ + KT V+M L+ A +L+T IP Sbjct: 240 ESASIAVVWAFFVTMFIYRDYKWRDLPKLVHRTVKTVTVVMILIGFAAAFGYLMTMMMIP 299 Query: 299 SEITGFISPLIDRPTLLMFVIMLVVLVVGTALDLTPTILILTPVLMPIIKQAGIDPVYFG 358 ++T F++ L D +++ +I +++L++G +D++P ILILTP+L+P++K G+DPV+FG Sbjct: 300 MKVTAFLTSLSDNKYVILAMINIMLLLLGCLMDMSPLILILTPILLPVVKMLGVDPVHFG 359 Query: 359 VLFIMNTCIGLLTPPVGVVLNVVSGVGRVPLGKVIVGVTPFLVAQILVLFLLVLFPDI 416 ++ ++N IGL+TPPVG VL + V ++PLG V + PF VA +VL ++ P I Sbjct: 360 MIMMVNLGIGLITPPVGTVLFTGAAVAKLPLGIVTRAMMPFFVALFVVLLMVTYVPAI 417 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: 444 Number of extensions: 18 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: 425 Length of database: 427 Length adjustment: 32 Effective length of query: 393 Effective length of database: 395 Effective search space: 155235 Effective search space used: 155235 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