Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate PfGW456L13_1569 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1569 Length = 372 Score = 230 bits (586), Expect = 6e-65 Identities = 147/358 (41%), Positives = 196/358 (54%), Gaps = 17/358 (4%) Query: 4 LELRNVNKTYGPGL--PDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGGA 61 + +R+V K YG P LK+I+L I D EF L+GPSGCGK+TL+ IAG E + G Sbjct: 12 VSIRSVRKVYGDPKTGPVALKSIDLDIRDNEFFTLLGPSGCGKTTLLRMIAGFEFPTEGE 71 Query: 62 ILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTA----EIDEEVA 117 IL+ +I+ P R + VFQ YAL+P M++ +N+AFGL+ M ++ E V Sbjct: 72 ILLYGENIADRPPFQRPVNTVFQHYALFPHMTIAENLAFGLESHPMGKVLHKTQLAERVR 131 Query: 118 RVSKLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTE 177 + L+Q+E +RKP QLSGGQQQRVA+ RALA PK+ L DEPLS LD KLR MR E Sbjct: 132 EMLALVQMERFANRKPAQLSGGQQQRVALARALAPHPKVLLLDEPLSALDLKLRQAMREE 191 Query: 178 MKLMHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIG 237 +K + R T ++VTHDQ EA+T+ D++AV+ +G +QQ G P+DIY P N FVA FIG Sbjct: 192 LKTIQARTGITFIFVTHDQEEALTMSDRIAVLSEGEVQQVGRPEDIYERPRNRFVADFIG 251 Query: 238 SPPMNFIPLRLQRKDGRLLALLDSGQARCELPLGMQDAGLEDREVILGIRPEQIILANGE 297 NFI + R + L +G A LP V L +RPE++ L Sbjct: 252 E--TNFIEGTVTRVEDGLAWF--AGPAGHPLPAQPCSDVRVGANVTLSVRPERLHLVPAT 307 Query: 298 ANGLPTIRAEVQVTEPTGPDTLVFVNLNDTKVCCRLAPDVAP-----AVGETLTLQFD 350 R E Q+ G D V+L+D P+ AVG L FD Sbjct: 308 TENALPCRIEAQIY--LGTDLQYQVSLSDGSRLTVRTPNCVDQSKRFAVGSQAGLLFD 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: 362 Number of extensions: 21 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