Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate GFF2761 HP15_2705 inner-membrane translocator
Query= uniprot:A0A165KER0 (358 letters) >FitnessBrowser__Marino:GFF2761 Length = 335 Score = 166 bits (419), Expect = 1e-45 Identities = 111/353 (31%), Positives = 177/353 (50%), Gaps = 46/353 (13%) Query: 1 MKNTKTNWIIGAVALLVLPLILQSFGNAW-VRIADLALLYVLLALGLNIVVGYAGLLDLG 59 M++ +I A+ L++LP L GN + + + +GLN++VG+AG + LG Sbjct: 6 MQSRLRGLVILALILVILPAFL---GNPFHYELVTQMAIIAATVVGLNLLVGFAGQISLG 62 Query: 60 YVAFYAVGAYLFALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAM---L 116 + F+ +GAY + T W +P + A GA+ + Sbjct: 63 HAGFFGLGAYFTGIATG-------------------TYGWSSVPALVVGAIVVGAIAWIV 103 Query: 117 GAPTLKLRGDYLAIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGK-- 174 G P L+L+G YL++ TL G II I LNN LT GP G+ + + ++FG +L Sbjct: 104 GRPILRLKGHYLSMATLAVGFIIAIILNN---ERALTGGPDGM-PVPAFEIFGWELSAFG 159 Query: 175 RLEVFGFDINSVTLYYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTR 234 R +FG I +Y V+++V+V L +S IGRA ++ E+AA +G+NT Sbjct: 160 RYSLFGITIEGFQAWYIFASVVLLVAVWFALNLIESPIGRALRSVHGSEVAASVVGVNTA 219 Query: 235 NMKLLAFGMGASFGGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGA 294 K L F + A + + G+++ FQGF++P S S++ + MVVLGG+G GVILGA Sbjct: 220 KYKSLVFVISAIYASLMGSLYAHFQGFITPAVASFEFSILFITMVVLGGMGSTFGVILGA 279 Query: 295 VLLSALPEVLRYVAGPLQAMTDGRLDSAILRQLLIALAMIIIMLLRPRGLWPS 347 V+L LP+VL D L ++ L +++ M+ P+GL P+ Sbjct: 280 VVLKLLPQVL--------------ADFQELEHVMFGLILMLTMIFMPKGLLPT 318 Lambda K H 0.328 0.144 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: 335 Number of extensions: 26 Number of successful extensions: 5 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: 358 Length of database: 335 Length adjustment: 29 Effective length of query: 329 Effective length of database: 306 Effective search space: 100674 Effective search space used: 100674 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: 49 (23.5 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