Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_084544685.1 H566_RS22525 ABC transporter ATP-binding protein
Query= uniprot:Q1MCU1 (463 letters) >NCBI__GCF_000482785.1:WP_084544685.1 Length = 403 Score = 261 bits (666), Expect = 4e-74 Identities = 156/316 (49%), Positives = 201/316 (63%), Gaps = 29/316 (9%) Query: 143 LIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLSSY----------------FGL 186 L+YVMLA GLNIVVG AGLLDLGY+AFYAVGAY Y LL+S + Sbjct: 66 LLYVMLALGLNIVVGFAGLLDLGYIAFYAVGAYMYGLLASPHLTDTFPAIAALVPDGMHV 125 Query: 187 SFWVLLPLSGIFAALWGVILGFPVLRLRGDYLAIVTLAFGEIIRLVLINWT---DVTKGT 243 W ++PL+G AAL+GV+LG P L+LRGDYLAIVTL FGEIIR+ ++N ++T G Sbjct: 126 PVWFVIPLAGGLAALFGVLLGAPTLKLRGDYLAIVTLGFGEIIRIFMLNLNQPLNITNGP 185 Query: 244 FGISSIPKATLFGIPFDATAGGFAKLFHLPISSAYYKIFLFYLILALCMLTAYVTIRLRR 303 GI+ I FG D + G +LF + Y F +Y+ L L +LT RL+ Sbjct: 186 QGINLIDPIA-FG---DFSLGKRHELFGTKYAGTY---FYYYVFLGLTVLTIIACNRLQD 238 Query: 304 MPIGRAWEALREDEIACRSLGINTVTTKLTAFATGAMFAGFAGSFFAARQGFVSPESFVF 363 IGRAW A+REDEIA +++GINT KL AFA GA F G AGS FAA QGF+SPESF Sbjct: 239 SRIGRAWMAIREDEIAAKAMGINTRNIKLLAFAMGASFGGVAGSMFAAFQGFISPESFSL 298 Query: 364 LESAVILAIVVLGGMGSLTGIAIAAIVMVGGTELLREMS--FLKLIFGPDFT-PELYRML 420 +ES V+LA+VVLGGMG + G+ A+++ E LR ++ + IFG E+ RML Sbjct: 299 MESIVVLAMVVLGGMGHIPGVVFGAVLLAVFPEALRYVAGPVQEAIFGSVLVDAEVLRML 358 Query: 421 IFGLAMVVVMLFKPRG 436 I+G+AMV +ML +P+G Sbjct: 359 IYGVAMVAIMLLRPKG 374 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: 591 Number of extensions: 31 Number of successful extensions: 4 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: 463 Length of database: 403 Length adjustment: 32 Effective length of query: 431 Effective length of database: 371 Effective search space: 159901 Effective search space used: 159901 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 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