Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate AO353_25420 AO353_25420 spermidine/putrescine ABC transporter ATP-binding protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25420 Length = 372 Score = 232 bits (591), Expect = 1e-65 Identities = 148/361 (40%), Positives = 200/361 (55%), Gaps = 15/361 (4%) Query: 4 LELRNVNKTYGP--GLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGGA 61 + +R V K YG P LK+I+L I D EF L+GPSGCGK+TL+ IAG E + G Sbjct: 12 VSIRAVRKVYGDPHSGPVALKSIDLDIRDNEFFTLLGPSGCGKTTLLRMIAGFEFPTQGE 71 Query: 62 ILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKM----PTAEIDEEVA 117 IL+ +I+ P R + VFQ YAL+P M++ +N+AFGL+ M A+I E V Sbjct: 72 ILLYGENIADRPPYQRPVNTVFQHYALFPHMTIAENLAFGLESHPMGKVLSKAQIAERVR 131 Query: 118 RVSKLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTE 177 + L+Q+E +R+P QLSGGQQQRVA+ RALA PK+ L DEPLS LD KLR MR E Sbjct: 132 EMLALVQMERFATRRPTQLSGGQQQRVALARALAPHPKVLLLDEPLSALDLKLRQAMREE 191 Query: 178 MKLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIG 237 +K + + T ++VTHDQ EA+T+ D++AV+ +G +QQ G P+DIY P N FVA FIG Sbjct: 192 LKAIQAKTGITFIFVTHDQEEALTMSDRIAVLSEGEVQQVGRPEDIYERPRNRFVADFIG 251 Query: 238 SPPMNFIPLRLQRKDGRLLALLDSGQARCELPLGMQDAGLEDREVILGIRPEQIILANGE 297 NFI + + L +G A LP V L +RPE++ L Sbjct: 252 E--TNFIEGTVTHVEAGLAWF--AGPAGHPLPAQPCSDVNVGATVALSVRPERLHLLPAN 307 Query: 298 ANGLPTIRAEVQVTEPTGPDTLVFVNLNDTKVCCRLAPDVAPAVGETLTLQFDPAKVLLF 357 +G R + Q+ G D V+LND RL +V ++L LLF Sbjct: 308 TDGALPCRIDAQIY--LGTDLQYQVSLNDGS---RLTVRTPNSVDQSLRFAVGSQAGLLF 362 Query: 358 D 358 D Sbjct: 363 D 363 Lambda K H 0.319 0.138 0.393 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: 13 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: 386 Length of database: 372 Length adjustment: 30 Effective length of query: 356 Effective length of database: 342 Effective search space: 121752 Effective search space used: 121752 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 (21.7 bits) S2: 50 (23.9 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