Align TRAP-type large permease component (characterized, see rationale)
to candidate WP_086510167.1 BZY95_RS12010 TRAP transporter large permease
Query= uniprot:Q930R2 (425 letters) >NCBI__GCF_002151265.1:WP_086510167.1 Length = 423 Score = 322 bits (825), Expect = 1e-92 Identities = 168/414 (40%), Positives = 265/414 (64%), Gaps = 1/414 (0%) Query: 1 MTLVVFIVSLLGAMAIGVPVAFSLMFCGVVLMWYMGMFNTQIIAQNMIAGADTFTLLAIP 60 M L++F++ L+ IGVP+AFSL + +W + I+AQ I ++F L+AIP Sbjct: 1 MALLLFLL-LIVLFVIGVPIAFSLGLASAITVWQGELMPMLIVAQQYITSVNSFPLMAIP 59 Query: 61 FFILAGELMNAGGLSRRIIDFAIACVGHIRGGLGIVAIMAAVIMASISGSAAADTAALAA 120 FFILAG LM +GG+SRR++DF+ VG + GGL +VAI+ ++ A+ISGS AA TAA+ A Sbjct: 60 FFILAGYLMQSGGISRRLVDFSNTIVGSMTGGLAMVAIVTSLFFAAISGSGAATTAAIGA 119 Query: 121 ILIPMMAKAGYNVPRSAGLIAAGGVIAPVIPPSMAFIVFGVAANVSITQLFMAGIVPGLI 180 ILIP M GY +A AA G + +IPPS+ I++G+AANVS+ +F+AGI+PGL+ Sbjct: 120 ILIPAMIAKGYASGYAAANQAASGALGVIIPPSIPLILYGIAANVSVGDMFVAGILPGLM 179 Query: 181 MGIALVATWLLVVRKDDIQPLPRTPMKERVGATGRALWALGMPVIILGGIKAGVVTPTEA 240 + ++L+ R R+ +E A +AL A+ MPVIILGGI G+ TPTEA Sbjct: 180 ITLSLLLFAYGYARYHGHGGGERSSWREMFTAGRKALLAILMPVIILGGIYGGIFTPTEA 239 Query: 241 AVVAAVYALFVGMVIYRELKPRDLPGVILQAAKTTAVIMFLVCAALVSSWLITAANIPSE 300 AV+A VY+ VG VIYRE+ +D+ G++ +AA TTAV++ ++ AA + ++ + +PS Sbjct: 240 AVIAVVYSFLVGFVIYREISLKDIVGILQEAAVTTAVVLSIIGAAGLYGRILQSLRVPSM 299 Query: 301 ITGFISPLIDRPTLLMFVIMLVVLVVGTALDLTPTILILTPVLMPIIKQAGIDPVYFGVL 360 ++ F+ ID P L + ++ +++L+ G ++ ILI P+L+PI G DPV+FG++ Sbjct: 300 LSNFVIGAIDSPLLFIVLVNVLLLMAGMFIEAAAAILIFVPILLPIAVSFGFDPVHFGII 359 Query: 361 FIMNTCIGLLTPPVGVVLNVVSGVGRVPLGKVIVGVTPFLVAQILVLFLLVLFP 414 ++N +G+ TPPVG+ L V S + +V + ++ + PF+ ++ LF++ + P Sbjct: 360 MVVNLAMGMFTPPVGLNLFVASQISKVGVARLTWSILPFVAIVLVNLFIISVVP 413 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: 502 Number of extensions: 22 Number of successful extensions: 2 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: 423 Length adjustment: 32 Effective length of query: 393 Effective length of database: 391 Effective search space: 153663 Effective search space used: 153663 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 24 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