Align TRAP-type large permease component (characterized, see rationale)
to candidate Echvi_3627 Echvi_3627 TRAP transporter, DctM subunit
Query= uniprot:Q930R2 (425 letters) >FitnessBrowser__Cola:Echvi_3627 Length = 431 Score = 308 bits (788), Expect = 3e-88 Identities = 162/421 (38%), Positives = 260/421 (61%), Gaps = 4/421 (0%) Query: 1 MTLVVFIVSLLGAMAIGVPVAFSLMFCGVV--LMWYMGMFNTQIIAQNMIAGADTFTLLA 58 +T+++ ++S + M +GVPVA+SL F ++ ++ + + IAQ M AG ++F+LLA Sbjct: 4 ITIIILVLSFITLMGLGVPVAWSLGFSSLLTLMVTVAAVPSMTTIAQRMGAGLNSFSLLA 63 Query: 59 IPFFILAGELMNAGGLSRRIIDFAIACVGHIRGGLGIVAIMAAVIMASISGSAAADTAAL 118 IPFFILAGE+MN GG++ R+I+ A A G + GGL V ++AA++ +I+GSA A +AL Sbjct: 64 IPFFILAGEIMNKGGIANRLINLAKALTGKLPGGLLYVNVIAAMLFGAIAGSAVAAASAL 123 Query: 119 AAILIPMMAKAGYNVPRSAGLIAAGGVIAPVIPPSMAFIVFGVAAN-VSITQLFMAGIVP 177 IL M GY + VIPPS IV+ +A+ VSI LF+AG +P Sbjct: 124 GGILGKRMEDEGYPKELGVAVNVTSSTTGLVIPPSNVLIVYSLASGGVSIAALFVAGYIP 183 Query: 178 GLIMGIALVATWLLVVRKDDIQPLPRTPMKERVGATGRALWALGMPVIILGGIKAGVVTP 237 GL MG+ L+ T ++K + T KE A +L + VI++GGI GV T Sbjct: 184 GLFMGLLLMLTAAYFIKKKKLPAGEPTSFKELGKVFFSAAPSLTLLVIVIGGIVMGVFTA 243 Query: 238 TEAAVVAAVYALFVGMVIYRELKPRDLPGVILQAAKTTAVIMFLVCAALVSSWLITAANI 297 TEA+ +A +Y L + Y ELKPRDLP ++L+++ TTAV+ L+ ++ SW++++ +I Sbjct: 244 TEASAIAVLYCLGLSF-FYGELKPRDLPAILLKSSATTAVVAMLIATSMAMSWVMSSEDI 302 Query: 298 PSEITGFISPLIDRPTLLMFVIMLVVLVVGTALDLTPTILILTPVLMPIIKQAGIDPVYF 357 P I+ + L D +++ +I L++L VG +D+TP +LI TP+ +P++ + GIDPV+F Sbjct: 303 PQSISAVLLSLSDNKFVILIIINLILLFVGIFMDMTPAVLIFTPIFLPVVTELGIDPVHF 362 Query: 358 GVLFIMNTCIGLLTPPVGVVLNVVSGVGRVPLGKVIVGVTPFLVAQILVLFLLVLFPDIV 417 G++ ++N CIGL TPPVG VL + GV + + V+ + PF +A I+ L ++ ++P + Sbjct: 363 GIIMVLNLCIGLCTPPVGSVLFIGVGVAKTSISNVVKPLLPFFIAMIIGLAVITIWPQLT 422 Query: 418 I 418 + Sbjct: 423 L 423 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: 485 Number of extensions: 24 Number of successful extensions: 4 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: 431 Length adjustment: 32 Effective length of query: 393 Effective length of database: 399 Effective search space: 156807 Effective search space used: 156807 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