Align TRAP-type large permease component (characterized, see rationale)
to candidate HSERO_RS19060 HSERO_RS19060 ABC transporter permease
Query= uniprot:Q930R2 (425 letters) >FitnessBrowser__HerbieS:HSERO_RS19060 Length = 627 Score = 226 bits (576), Expect = 2e-63 Identities = 128/423 (30%), Positives = 224/423 (52%), Gaps = 10/423 (2%) Query: 3 LVVFIVSLLGA-MAIGVPVAFSLMFCGVVLMWYMGMFNT---QIIAQNMIAGADTFTLLA 58 L+VF V L+G +A G+P+AF+ G M Y+ + T I+ M G + LL+ Sbjct: 205 LIVFFVLLIGVCVAGGIPIAFAF---GTATMAYLALATTAPLMIVVSRMDEGMSSLILLS 261 Query: 59 IPFFILAGELMNAGGLSRRIIDFAIACVGHIRGGLGIVAIMAAVIMASISGSAAADTAAL 118 +P F+L G L+ GL++ +IDF A +GH+RGGL V + A +++ ISGS AAD AA+ Sbjct: 262 VPLFVLLGSLLEMSGLAKTLIDFMAALLGHVRGGLQYVLLGAMFLVSGISGSKAADMAAI 321 Query: 119 AAILIPMMAKAGYNVPRSAGLIAAGGVIAPVIPPSMAFIVFGVAANVSITQLFMAGIVPG 178 A L P M K G L+++ G + IPPS+ I G +VSIT LF+ G++P Sbjct: 322 APALFPEMKKRGSKPEELVALLSSSGAMTETIPPSLVLITIGAVCSVSITALFIGGLMPA 381 Query: 179 LIMGIALVATWLLVVRKDDIQPLPRTPMKERVGATGRALWALGMPVIILGGIKAGVVTPT 238 I IA+ + R++ + + R P+ V A A+ AL +P++I + GV T T Sbjct: 382 AIATIAIAVVCWMRARREPMPDVKRAPLSLIVKALIAAIPALALPMLIRVAVIEGVATAT 441 Query: 239 EAAVVAAVYALFVGMVIY---RELKPRDLPGVILQAAKTTAVIMFLVCAALVSSWLITAA 295 E A + Y + VG++++ R L + L +++++A + I+ ++ A +W +T + Sbjct: 442 EVATIGVAYTVVVGLIMHLFMRHLSFKRLYPMLIESAALSGAILLIIGMATAMAWALTQS 501 Query: 296 NIPSEITGFISPLIDRPTLLMFVIMLVVLVVGTALDLTPTILILTPVLMPIIKQAGIDPV 355 +++ + + + + +++ +V+G+ L+ P I++ P+L P+ + G+ V Sbjct: 502 GFSAKLVALMQGVPGGGVGFLLITIVIFIVLGSLLEGIPAIVLFGPLLFPVARSLGVHDV 561 Query: 356 YFGVLFIMNTCIGLLTPPVGVVLNVVSGVGRVPLGKVIVGVTPFLVAQILVLFLLVLFPD 415 ++ ++ I+ IGL PP GV +G+V V V +L A ++ L ++ P Sbjct: 562 HYAMVVILAMGIGLFAPPFGVGFYAACAIGKVSPDGVFNRVWGYLAALVVALLVVAFVPW 621 Query: 416 IVI 418 I I Sbjct: 622 ISI 624 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: 611 Number of extensions: 29 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: 627 Length adjustment: 35 Effective length of query: 390 Effective length of database: 592 Effective search space: 230880 Effective search space used: 230880 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: 52 (24.6 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