Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_004306170.1 C665_RS09035 ABC transporter ATP-binding protein
Query= uniprot:A0A165KER0 (358 letters) >NCBI__GCF_000310185.1:WP_004306170.1 Length = 373 Score = 397 bits (1021), Expect = e-115 Identities = 202/347 (58%), Positives = 259/347 (74%), Gaps = 17/347 (4%) Query: 4 TKTNWIIGAVALLVLPLILQSFGNAWVRIADLALLYVLLALGLNIVVGYAGLLDLGYVAF 63 T W+I VA+ P I FG +WVRI D ALLY++LALGLN+VVG+AGLLDLGY+AF Sbjct: 17 TAARWLIILVAIAA-PFIAWQFGRSWVRILDFALLYMMLALGLNLVVGFAGLLDLGYIAF 75 Query: 64 YAVGAYLFALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKL 123 YAVGAY FA +ASPH +H W+++P+ A AA G MLG P L+L Sbjct: 76 YAVGAYTFAFLASPHF-------------DVHLPFWVILPLGAAFAALAGVMLGFPVLRL 122 Query: 124 RGDYLAIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVF-GFD 182 RGDYLAIVTLGFGEI+RIF+ NL++PVN+TNGP+G+ ID + +FG DL + + + F Sbjct: 123 RGDYLAIVTLGFGEIVRIFMLNLNYPVNITNGPQGINMIDPINLFGWDLSRNIRIGEDFT 182 Query: 183 INSVTLYYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAFG 242 I+S+ LYYY FL VV S+I RLQ SRIGRAW A+R+DE+AAKA+GINTR+MKLLAF Sbjct: 183 IHSLFLYYYFFLAAVVASIIFIQRLQISRIGRAWAAMRDDELAAKAIGINTRDMKLLAFA 242 Query: 243 MGASFGGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALPE 302 +GA+FGGV+GA+FGAFQGFVSPESFSLMES+ ++ MVV GG+G++ G ++GA +L+ LPE Sbjct: 243 LGATFGGVAGALFGAFQGFVSPESFSLMESIAVLTMVVFGGMGNLAGAVVGAFVLALLPE 302 Query: 303 VLRYVAGPLQAMTDGR--LDSAILRQLLIALAMIIIMLLRPRGLWPS 347 +LR VA PLQ G LD +LR LL++LAMI++MLLRP G+ P+ Sbjct: 303 LLRDVAVPLQQTLFGHVLLDPEVLRMLLLSLAMILMMLLRPAGMIPA 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: 434 Number of extensions: 18 Number of successful extensions: 3 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: 373 Length adjustment: 30 Effective length of query: 328 Effective length of database: 343 Effective search space: 112504 Effective search space used: 112504 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