Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_011767454.1 AZO_RS18725 ABC transporter ATP-binding protein
Query= uniprot:A0A165KER0 (358 letters) >NCBI__GCF_000061505.1:WP_011767454.1 Length = 365 Score = 394 bits (1011), Expect = e-114 Identities = 201/343 (58%), Positives = 256/343 (74%), Gaps = 17/343 (4%) Query: 8 WIIGAVALLVLPLILQSFGNAWVRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVG 67 W+I +A+ PLI FG +WVRI D ALLY++LALGLN+VVG+AGLLDLGY+AFYAVG Sbjct: 21 WLILILAIAA-PLIAWQFGRSWVRILDFALLYMMLALGLNLVVGFAGLLDLGYIAFYAVG 79 Query: 68 AYLFALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDY 127 AY FA +ASPH +H W+++P+ A AA G LG P L+LRGDY Sbjct: 80 AYSFAFLASPHF-------------DVHLPFWLILPLGAGFAALAGIALGFPVLRLRGDY 126 Query: 128 LAIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVFG-FDINSV 186 LAIVTLGFGEI+RIF+ NL++P+N+TNGP+G+ ID + +FG DL + + V INS+ Sbjct: 127 LAIVTLGFGEIVRIFMLNLNYPINITNGPQGINMIDPIVLFGWDLSRNIRVTEELSINSL 186 Query: 187 TLYYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAFGMGAS 246 LYYY FL V S+I RLQ SRIGRAW A+R+DE+AAKA+GINTRNMKLLAF +GA+ Sbjct: 187 FLYYYFFLAFVAGSIIFIRRLQISRIGRAWAAMRDDELAAKAIGINTRNMKLLAFALGAT 246 Query: 247 FGGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALPEVLRY 306 FGGVSG +FGAFQGFVSPESFSLMES+ ++ MVV GG+G+I G ++GA +L+ LPE+LR+ Sbjct: 247 FGGVSGCLFGAFQGFVSPESFSLMESIAVLTMVVFGGMGNIAGALVGAFVLALLPEILRH 306 Query: 307 VAGPLQAMTDGR--LDSAILRQLLIALAMIIIMLLRPRGLWPS 347 +A PLQ G LD +LR LL++LAMI++MLLRP GL P+ Sbjct: 307 IAVPLQQAVFGHVLLDPEVLRMLLLSLAMILMMLLRPAGLIPA 349 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: 446 Number of extensions: 20 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: 358 Length of database: 365 Length adjustment: 29 Effective length of query: 329 Effective length of database: 336 Effective search space: 110544 Effective search space used: 110544 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 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