Align TRAP transporter, subunit DctM (characterized, see rationale)
to candidate Ac3H11_3955 TRAP-type C4-dicarboxylate transport system, large permease component
Query= uniprot:I7DRS6 (467 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3955 Length = 427 Score = 293 bits (750), Expect = 8e-84 Identities = 174/464 (37%), Positives = 262/464 (56%), Gaps = 44/464 (9%) Query: 1 MDVVLLFSMVIGLLLIGVPIAVALGLSS---TLFLLIYSDSSLASVAGTLFEAFEGHFTL 57 MD ++L L++IGVPIA +LGLS+ L++ + D+ + VA + F+L Sbjct: 1 MDTLVLLGTFFVLMMIGVPIAYSLGLSALAGALWIDLPLDAVMIQVASGV-----NKFSL 55 Query: 58 LAIPFFILASSFMTTGGVARRIIRFSIACVGHLPGGLAIAGVFACMLFAALSGSSPATVV 117 LAIPFF+LA + M GG+ARR++ F+ VG + GGL++ + A F A+SGSS A Sbjct: 56 LAIPFFVLAGAIMAEGGMARRLVAFAGVLVGFIRGGLSLVNILASTFFGAISGSSVADTA 115 Query: 118 AIGSIVIAGMRQVGYSKEFAAGVICNAGTLGILIPPSIVMVVY--AAAVEVSVGRMFLAG 175 +IGS++I M + GY + FA V + ILIPPS V+Y AA VS+ +F+AG Sbjct: 116 SIGSVLIPEMEKKGYPRPFATAVTVSGSVQAILIPPSHNAVLYSLAAGGTVSIAALFMAG 175 Query: 176 VIPGLMAGLMLMVTIYVMAKVKNLPKGEWLGWGEVAASAANASVGLLLIGIILGGIYGGI 235 V+PGL+ GL L A + PKGE + + A GL+ + IILGGI G+ Sbjct: 176 VLPGLLMGLTLAALCLFTAHREGYPKGEVIPLKQALKICVEALWGLMTMVIILGGILSGV 235 Query: 236 FTPTEAAAVASVYAFFVATFVYRDMGPLKSAPKPKDMGQFLTMLPKMLGQTVVYFIPSFF 295 FT E+A++A V+AFFV F+YRD K +D LPK++ +TV Sbjct: 236 FTANESASIAVVWAFFVTMFIYRDY-------KWRD-------LPKLVHRTV-------- 273 Query: 296 HADTRHALFEAGKLTVTLLFVIANALILKHVLTDEQVPQQIATAMLSAGFGPVMFLIVVN 355 K ++ +I A +++T +P ++ + S + L ++N Sbjct: 274 ------------KTVTVVMILIGFAAAFGYLMTMMMIPMKVTAFLTSLSDNKYVILAMIN 321 Query: 356 VILLIGGQFMEPSGLLVIVAPLVFPIAIELGIDPIHLGIIMVVNMEIGMITPPVGLNLFV 415 ++LL+ G M+ S L++I+ P++ P+ LG+DP+H G+IM+VN+ IG+ITPPVG LF Sbjct: 322 IMLLLLGCLMDMSPLILILTPILLPVVKMLGVDPVHFGMIMMVNLGIGLITPPVGTVLFT 381 Query: 416 TSGVAGMPMMAVVRAALPFLAVLFVFLIMITYIPWISTVLPNAV 459 + VA +P+ V RA +PF LFV L+M+TY+P IS LP A+ Sbjct: 382 GAAVAKLPLGIVTRAMMPFFVALFVVLLMVTYVPAISLWLPRAM 425 Lambda K H 0.329 0.144 0.421 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: 612 Number of extensions: 37 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: 467 Length of database: 427 Length adjustment: 33 Effective length of query: 434 Effective length of database: 394 Effective search space: 170996 Effective search space used: 170996 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 (21.8 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