Align TreT, component of Trehalose porter (characterized)
to candidate SMa1339 SMa1339 ABC transporter permease
Query= TCDB::Q97ZC2 (275 letters) >FitnessBrowser__Smeli:SMa1339 Length = 301 Score = 118 bits (295), Expect = 2e-31 Identities = 88/276 (31%), Positives = 136/276 (49%), Gaps = 25/276 (9%) Query: 10 LLVLPALAYVISFAFFPTIEAVYLSFQD-------PHGGFSLYNYKELS-----YFNLSS 57 L ++P + ++I F FP I ++ SF D P L NY+EL + N + Sbjct: 28 LFIIPTILFLIVFNIFPLIYSLGYSFTDFRASTNAPATFVGLQNYRELLNDPFIWANFAI 87 Query: 58 AIINTIVVTIGALAIQLALGFLVASVLSREFFGKRALSTITIIPMGIATVVAAVTFSFVF 117 IV G Q+ +GF A +L+RE K ++T+ ++PM ++ V + + ++ Sbjct: 88 TAKYVIVSVTG----QVVVGFGTAMLLNREIPFKGLITTLLLLPMMLSMAVVGLFWKLLY 143 Query: 118 QTSGGYANTILHSLFGL-NVNWYQSSISSLLVVMIADSWKNTPIVALILLAGMSSIPKEL 176 S G N L GL + W + +L V I D W +P V L+ LAG+S++P+ L Sbjct: 144 DPSFGIINYAL----GLGSFEWLANPEMALYAVAITDIWMWSPFVMLLSLAGLSAVPRHL 199 Query: 177 YYASAIDGAGPIRRFFYITLPNLRSFIGISLILRGVQEFNIFALPLILIGEHPPLLTTLI 236 Y A+AID AGP FF ITLP + + I++I R ++ F F L IL + P + Sbjct: 200 YEAAAIDRAGPFYTFFRITLPLVAPILMIAIIFRTMEAFKTFDLAYILTSQ--PTTEVIS 257 Query: 237 YDLYTTTFPE--VGLALASATILLGFILVFSGIVIK 270 LY F E G + A A I+L +L + I +K Sbjct: 258 IRLYKMAFQEWQTGRSCALAYIVLIMVLAITNIYVK 293 Lambda K H 0.328 0.143 0.414 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: 185 Number of extensions: 9 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: 275 Length of database: 301 Length adjustment: 26 Effective length of query: 249 Effective length of database: 275 Effective search space: 68475 Effective search space used: 68475 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 (21.7 bits) S2: 47 (22.7 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