Align TRAP-type large permease component (characterized, see rationale)
to candidate 8501197 DvMF_1931 TRAP dicarboxylate transporter, DctM subunit (RefSeq)
Query= uniprot:Q930R2 (425 letters) >FitnessBrowser__Miya:8501197 Length = 640 Score = 298 bits (764), Expect = 2e-85 Identities = 155/404 (38%), Positives = 247/404 (61%), Gaps = 1/404 (0%) Query: 14 MAIGVPVAFSLMFCGVVLMWYMGMFNTQIIAQNMIAGADTFTLLAIPFFILAGELMNAGG 73 + +GVP+AFSL + + G + +AQ D+F +LAIPFFI AG M AGG Sbjct: 232 LLVGVPIAFSLGLATIATVLGAGTLPLEYLAQIAFVSIDSFPILAIPFFIAAGVFMGAGG 291 Query: 74 LSRRIIDFAIACVGHIRGGLGIVAIMAAVIMASISGSAAADTAALAAILIPMMAKAGYNV 133 LSRR++ VG + GG+ + I+ + A+ISGS A AA+ +I IP M + GY+ Sbjct: 292 LSRRLLALGDELVGALPGGMALATIVTCMFFAAISGSGPATVAAIGSITIPAMVERGYDK 351 Query: 134 PRSAGLIAAGGVIAPVIPPSMAFIVFGVAANVSITQLFMAGIVPGLIMGIALVAT-WLLV 192 +A ++A+ G I +IPPS F+V+GVAA S+ +LF+AGIVPG++ G+AL+A + + Sbjct: 352 FFAAAVVASAGCIGVMIPPSNPFVVYGVAAQASVGKLFLAGIVPGVLCGLALMAVAYYIS 411 Query: 193 VRKDDIQPLPRTPMKERVGATGRALWALGMPVIILGGIKAGVVTPTEAAVVAAVYALFVG 252 ++K + + A A WAL +PVI+LGGI G++TPTEAA V+A+Y + VG Sbjct: 412 LKKGWRGEARHRDFRSVMQAMWEAKWALLVPVIVLGGIYGGIMTPTEAAAVSALYGMIVG 471 Query: 253 MVIYRELKPRDLPGVILQAAKTTAVIMFLVCAALVSSWLITAANIPSEITGFISPLIDRP 312 + IYRE+ R + ++++A+T++VI+ L+ A + ++T +P I I + Sbjct: 472 LFIYREITWRRMWDCMVESAQTSSVIIVLMAMATLFGNIMTIEQVPDHIAAMILGVTSNK 531 Query: 313 TLLMFVIMLVVLVVGTALDLTPTILILTPVLMPIIKQAGIDPVYFGVLFIMNTCIGLLTP 372 ++ +I + +L VGT ++ I+I+TP+L+P++ Q G+DP++FGV+ ++N IG +TP Sbjct: 532 IAILLLINVFLLWVGTFMEALAAIVIITPILLPLVTQVGVDPIHFGVIMVVNLAIGFITP 591 Query: 373 PVGVVLNVVSGVGRVPLGKVIVGVTPFLVAQILVLFLLVLFPDI 416 PVGV L V S + +V +G V+ PFL+ I +L + P I Sbjct: 592 PVGVNLFVASSISKVSIGDVVRAAWPFLLVMIALLMAITYIPAI 635 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: 679 Number of extensions: 35 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 425 Length of database: 640 Length adjustment: 35 Effective length of query: 390 Effective length of database: 605 Effective search space: 235950 Effective search space used: 235950 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