Align Amino-acid permease RocE (characterized)
to candidate WP_011989216.1 CKL_RS03175 amino acid permease
Query= SwissProt::P39137 (467 letters) >NCBI__GCF_000016505.1:WP_011989216.1 Length = 411 Score = 267 bits (682), Expect = 6e-76 Identities = 142/398 (35%), Positives = 227/398 (57%), Gaps = 8/398 (2%) Query: 60 MFLTMLCLGELAVAFPVSGSFQTYATKFISPAFGFAFGWLYWLGWAVTCAIEFLSAGQLM 119 MF+ M LGELA ++PVSGSF YA +FI P G+ GW YW W VTC E + G + Sbjct: 1 MFIIMRALGELATSYPVSGSFSAYANEFIGPLAGYLTGWTYWFMWVVTCMAEITAVGVYV 60 Query: 120 QRWFPHIDVWIWCLVFAALMFILNAITTKAFAESEFWFSGIKILIILLFIILGGAAM-FG 178 + W P++ WI L +M +N I KA+ E EFWF+ IK++ I++ I LG + FG Sbjct: 61 KFWIPNMPQWIPALAALVIMTCVNLIAVKAYGEFEFWFALIKVVTIIIMIGLGLLMIIFG 120 Query: 179 LIDLKGGEQAPFLTHFYEDGLFPNGIKAMLITMITVNFAFQGTELIGVAAGESEDPEKTI 238 + + GG+ + G P G+ +++++ V FA+ GTELIGV AGE+++PEKTI Sbjct: 121 IGN--GGKPIGISNLWSHGGFLPKGLWGPMLSIVMVMFAYLGTELIGVTAGEAKNPEKTI 178 Query: 239 PRSIKQTVWRTLVFFVLSIIVIAGMIPWKQAGVVESPFVAVFEQIGIPYAADIMNFVILI 298 P ++ + WR LVF+V ++ VI + PW G + SPFV F ++GI AA I+NFV+L Sbjct: 179 PAAVNKVFWRILVFYVGALFVIMCLYPWNSLGTIGSPFVLTFNKLGISAAAGIINFVVLT 238 Query: 299 ALLSVANSGLYASTRILYAMANEGQAFKALGKTNQRGVPMYSLIVTMAVACLSLLTKFAQ 358 A LS NSG++++ R+LY ++ +G A K K N+ VP+ ++++ + ++ + Sbjct: 239 AALSSCNSGIFSTGRMLYNLSLQGSAPKVFSKLNKSHVPVTGIVISAFFLLIGVVLNYLV 298 Query: 359 AETVYMVLLSLAGMSAQVGWITISLSQIMFRRKYIREGGKIEDLKFKTPLYPVLPLIGLT 418 V+ + S+A A W + ++QI FR++ E +++ L F YP L I L Sbjct: 299 PGKVFTYVTSVATFGAIWVWGIVLVAQIKFRKRLNPE--EVKKLHFPVFGYPYLNWITLA 356 Query: 419 LNTVVLISLAFDPEQRIALYCG---VPFMIICYIIYHV 453 V+I + F+ + +A+ +I+CY ++ + Sbjct: 357 FLAFVVIMMFFNKDTLVAIIVAPIWFAILIVCYYVFGI 394 Lambda K H 0.329 0.142 0.438 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: 542 Number of extensions: 27 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: 467 Length of database: 411 Length adjustment: 32 Effective length of query: 435 Effective length of database: 379 Effective search space: 164865 Effective search space used: 164865 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