Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate 8501894 DvMF_2609 inner-membrane translocator (RefSeq)
Query= uniprot:Q1MCU1 (463 letters) >FitnessBrowser__Miya:8501894 Length = 415 Score = 315 bits (808), Expect = 1e-90 Identities = 183/380 (48%), Positives = 241/380 (63%), Gaps = 46/380 (12%) Query: 68 IGRFAMVVFIRPNIDRRKLSKAREGELDISTEKSFFHR---------HFLKIALIALLLY 118 +G F + R + R++ +A +S ++F R L + L A L+ Sbjct: 45 VGSFVLSFVWRFMLARKEAGRAAAAGGAMSARGAWFERLRSDPKAAVPALVVLLSAFLVL 104 Query: 119 PMVVVAIKGPQGSLTYVDNFGIQILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYSYA 178 P VV TY N I L+YVML GLNIVVGL+G L LGYVAFYAVGAYSYA Sbjct: 105 PWVVS---------TYQTNIMISALLYVMLGLGLNIVVGLSGQLVLGYVAFYAVGAYSYA 155 Query: 179 LLSSYFGLSFWVLLPLSGIFAALWGVILGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTD 238 +L+S FGL FW +LP+ G AAL+G++LGFPVLRLRGDYLAIVTL FGEIIRLVL NW+ Sbjct: 156 ILNSNFGLGFWSVLPIGGAMAALFGILLGFPVLRLRGDYLAIVTLGFGEIIRLVLENWSS 215 Query: 239 VTKGTFGISSIPKATLFGIPFDATAGGFAKLFHLPISSAYYKIFLFYLILALCMLTAYVT 298 ++G GI++I + L G+ L +S A +++YLILA ++T Sbjct: 216 FSQGPSGIANIERPGLLGM-------------QLSVSDA--TTYIYYLILAAVIVTILAV 260 Query: 299 IRLRRMPIGRAWEALREDEIACRSLGINTVTTKLTAFATGAMFAGFAGSFFAARQGFVSP 358 RL+ IGRAW+ALREDEIAC+++GI+ TTKLTAFA GA +AGFAG FAA+ F++P Sbjct: 261 TRLKNSRIGRAWQALREDEIACQAMGIDITTTKLTAFALGACWAGFAGVIFAAKTTFINP 320 Query: 359 ESFVFLESAVILAIVVLGGMGSLTGIAIAAIVMVGGTELLREMSFLKLIFGPDFTPELYR 418 SF FLESA++LA+VVLGGMGS+ G+++ A+V++ E LR S YR Sbjct: 321 ASFTFLESAMVLAMVVLGGMGSVIGVSVGALVLILLPEYLRAFS-------------EYR 367 Query: 419 MLIFGLAMVVVMLFKPRGFV 438 MLIFG MV++M+F+P+G V Sbjct: 368 MLIFGATMVLMMVFRPQGLV 387 Lambda K H 0.330 0.145 0.432 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: 571 Number of extensions: 29 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: 463 Length of database: 415 Length adjustment: 32 Effective length of query: 431 Effective length of database: 383 Effective search space: 165073 Effective search space used: 165073 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 (21.8 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