Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_041096493.1 SUTH_RS01370 ABC transporter ATP-binding protein
Query= uniprot:A0A165KER0 (358 letters) >NCBI__GCF_000828635.1:WP_041096493.1 Length = 350 Score = 396 bits (1017), Expect = e-115 Identities = 200/347 (57%), Positives = 254/347 (73%), Gaps = 15/347 (4%) Query: 12 AVALLVLPLILQSFGNAWVRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVGAYLF 71 AVAL+ LP +L S G AWVRI + A+L+VLL+LGLNIVVGYAGLLDLGYVAFYAVGAY++ Sbjct: 14 AVALIALPFVLASAGTAWVRITNFAVLFVLLSLGLNIVVGYAGLLDLGYVAFYAVGAYVY 73 Query: 72 ALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDYLAIV 131 AL+ASPH GLH W+++P+ A +A G +LGAPTL+LRGDYLAIV Sbjct: 74 ALLASPHF-------------GLHLPFWVILPIGAAVACVAGVILGAPTLRLRGDYLAIV 120 Query: 132 TLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGFDINSVTLYYY 191 TLGFGEI+RIF+NNL PVNLTNGPKG+ +ID ++ ++ + G + YYY Sbjct: 121 TLGFGEIVRIFMNNLSAPVNLTNGPKGINRIDPFQIGPVNFSSTDTLAGLAFSGPIKYYY 180 Query: 192 LFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAFGMGASFGGVS 251 L++++ ++I RLQDSRIGRAW+AIREDEIAAKA GINTRN+KLLAF MGASFGG++ Sbjct: 181 FLLLVLLAVIVINRRLQDSRIGRAWVAIREDEIAAKASGINTRNIKLLAFAMGASFGGIA 240 Query: 252 GAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALPEVLRYVAGPL 311 G MF A Q FVSPESF L ES+M++AMVVLGG+G+I GVI GA+LLS +PE+LRY P Sbjct: 241 GGMFAAMQTFVSPESFVLNESIMVLAMVVLGGMGNIWGVIAGALLLSFVPELLRYTVEPA 300 Query: 312 QAMTDGRL--DSAILRQLLIALAMIIIMLLRPRGLWPSPEHGKSLTQ 356 Q G+L D +LR L+ +A+++ M RP GLWP H + + + Sbjct: 301 QRALFGKLLVDPEVLRMLVFGVALVLTMRFRPAGLWPETRHRREMNE 347 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: 413 Number of extensions: 17 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: 350 Length adjustment: 29 Effective length of query: 329 Effective length of database: 321 Effective search space: 105609 Effective search space used: 105609 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 Apr 09 2024. 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