Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_050461645.1 AKL27_RS04815 ABC transporter ATP-binding protein
Query= uniprot:A0A165KER0 (358 letters) >NCBI__GCF_001189915.1:WP_050461645.1 Length = 405 Score = 454 bits (1169), Expect = e-132 Identities = 225/373 (60%), Positives = 284/373 (76%), Gaps = 24/373 (6%) Query: 2 KNTKTNWIIGAVALLVLPLILQSFGNAWVRIADLALLYVLLALGLNIVVGYAGLLDLGYV 61 + K + ++ ++V P I FGN+WVRI D+ALLY++LALGLN+VVG+AGLLDLGY+ Sbjct: 13 RQAKASLLVLLAIMIVFPFIASQFGNSWVRIMDVALLYIMLALGLNVVVGFAGLLDLGYI 72 Query: 62 AFYAVGAYLFALMASPHLADNFAAFAAMFP----------------NGLHTSLWIVIPVA 105 AFYA+GAY L+ASP A +F +P NG+H SLW+++P++ Sbjct: 73 AFYAIGAYTAGLLASPQFAAVIESFVNTYPMVGNFLIMICGPEIVQNGIHLSLWVIVPLS 132 Query: 106 ALLAAFFGAMLGAPTLKLRGDYLAIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSV 165 A++AA FGA+LGAPTLKLRGDYLAIVTLGFGEIIRIF+NNL+ PVN+TNGP+G+ ID + Sbjct: 133 AMVAALFGALLGAPTLKLRGDYLAIVTLGFGEIIRIFMNNLNAPVNITNGPQGINLIDPI 192 Query: 166 KVFGLDLGKR------LEVFGFDINSVTLYYYLFLVLVVVSVIICYRLQDSRIGRAWMAI 219 +VFG+ LG ++ G + SV YY+LFL+L + + RLQDSR+GRAW+AI Sbjct: 193 RVFGVSLGGEPGSGSIVKFLGMSMPSVNAYYFLFLLLCIAVIFFSIRLQDSRLGRAWVAI 252 Query: 220 REDEIAAKAMGINTRNMKLLAFGMGASFGGVSGAMFGAFQGFVSPESFSLMESVMIVAMV 279 REDEIAAKAMGINTRN+KLLAF MGASFGGV+GAMF +FQGFVSPESFSL ES+ ++AMV Sbjct: 253 REDEIAAKAMGINTRNIKLLAFAMGASFGGVAGAMFASFQGFVSPESFSLTESIAVLAMV 312 Query: 280 VLGGIGHIPGVILGAVLLSALPEVLRYVAGPLQAMTDGR--LDSAILRQLLIALAMIIIM 337 VLGGIGHIPGV+LG V+L+ALPE+LR+V PLQ M GR +D+ +LRQLL LAM++IM Sbjct: 313 VLGGIGHIPGVVLGGVILAALPEILRHVVEPLQMMIFGRVWIDAEVLRQLLYGLAMVVIM 372 Query: 338 LLRPRGLWPSPEH 350 L RP GLWPSP H Sbjct: 373 LNRPAGLWPSPRH 385 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: 491 Number of extensions: 15 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: 405 Length adjustment: 30 Effective length of query: 328 Effective length of database: 375 Effective search space: 123000 Effective search space used: 123000 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: 50 (23.9 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