Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate GFF4127 HP15_4067 spermidine/putrescine ABC transporter ATPase subunit
Query= reanno::Smeli:SMc04256 (361 letters) >FitnessBrowser__Marino:GFF4127 Length = 362 Score = 216 bits (550), Expect = 8e-61 Identities = 135/352 (38%), Positives = 194/352 (55%), Gaps = 11/352 (3%) Query: 13 FGAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQIFIKDRNVTWEEP 72 FG+ +D ++LD+ G F +LG SGCGK+TLL +AG G I I+ + P Sbjct: 14 FGSNAAVDHVSLDVPAGTFFSILGPSGCGKTTLLRLLAGFDKPDQGDIHIRGERMNDVPP 73 Query: 73 KDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASEILQIQPLLKRKPS 132 R + MVFQ AL+P MTV N+++GLK K+P E KR+ R E + + L R P Sbjct: 74 NRRPVNMVFQHLALFPTMTVGDNIAYGLKRRKMPLVERRKRIARVLEQVGLPDLEHRNPQ 133 Query: 133 ELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRLHQSLKNTMIYVTH 192 ELSGGQRQRVA+ R LV + + L DEPL LD KLR +++VE+K L + T +Y+TH Sbjct: 134 ELSGGQRQRVALARCLVLEPTLLLLDEPLGALDLKLREQMKVELKHLQKQFGTTFVYITH 193 Query: 193 DQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSMNFFRGE-VEPKDG 251 DQ EA+ ++D++AVM+ G Q+A P +Y P FVAGF+G N GE V +D Sbjct: 194 DQSEAMVMSDQVAVMRDGRFDQVAPPEELYREPATPFVAGFVG--DNNRLSGELVSVRDS 251 Query: 252 RSFVRA-GGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKV--DEARDGEPTHQAVVDIEE 308 + +R G+ V A LQ G + L +RPE + + D G + QA V Sbjct: 252 LAELRLDDGVL--VQGRVASDNLQAGHRAELYIRPESLVLSGDALSPGFSSMQAKVRTTL 309 Query: 309 PMGADNLLWLTFAGQSMSVRI---AGQRRYPPGSTVRLSFDMGVASIFDAES 357 GA++ + GQ + R+ R S++RL+++ +A +F AES Sbjct: 310 FDGANSRVEAETCGQPVYARLPQDGSAPRLSVDSSIRLAWNPSLARVFGAES 361 Lambda K H 0.320 0.137 0.392 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: 352 Number of extensions: 17 Number of successful extensions: 2 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: 361 Length of database: 362 Length adjustment: 29 Effective length of query: 332 Effective length of database: 333 Effective search space: 110556 Effective search space used: 110556 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 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