Align D-trehalose PTS system, I, HPr, and IIA components (characterized)
to candidate GFF4500 PS417_23035 PTS mannose transporter subunit IIC
Query= reanno::WCS417:GFF4500 (838 letters) >FitnessBrowser__WCS417:GFF4500 Length = 838 Score = 1602 bits (4149), Expect = 0.0 Identities = 838/838 (100%), Positives = 838/838 (100%) Query: 1 MTTTQPLELLAPLSGVLLALDKVPDPVFSSRLIGDGLCIDPTSQTLCAPLAGVISNIQDS 60 MTTTQPLELLAPLSGVLLALDKVPDPVFSSRLIGDGLCIDPTSQTLCAPLAGVISNIQDS Sbjct: 1 MTTTQPLELLAPLSGVLLALDKVPDPVFSSRLIGDGLCIDPTSQTLCAPLAGVISNIQDS 60 Query: 61 GHAVSITDDNGVQVLMHIGLDTVNLAGQGFTRLVQEGQRVEAGQPLIEFDADYVALNARS 120 GHAVSITDDNGVQVLMHIGLDTVNLAGQGFTRLVQEGQRVEAGQPLIEFDADYVALNARS Sbjct: 61 GHAVSITDDNGVQVLMHIGLDTVNLAGQGFTRLVQEGQRVEAGQPLIEFDADYVALNARS 120 Query: 121 LLTLMLVVSGEPFSLLADGLVETGQPLLQLSPSGAVEAVDEEEGDALFSKPLTLPNANGL 180 LLTLMLVVSGEPFSLLADGLVETGQPLLQLSPSGAVEAVDEEEGDALFSKPLTLPNANGL Sbjct: 121 LLTLMLVVSGEPFSLLADGLVETGQPLLQLSPSGAVEAVDEEEGDALFSKPLTLPNANGL 180 Query: 181 HARPAAVFAQAAKGFNASIYLHKQTQSANAKSLVAIMALQTVQGDTLQVSAAGEDAEAAI 240 HARPAAVFAQAAKGFNASIYLHKQTQSANAKSLVAIMALQTVQGDTLQVSAAGEDAEAAI Sbjct: 181 HARPAAVFAQAAKGFNASIYLHKQTQSANAKSLVAIMALQTVQGDTLQVSAAGEDAEAAI 240 Query: 241 KALVALLAEGCGEAVVNVAEPVATQSSATLLRGVCASPGSAFGQVVQVTDPELVITEQGT 300 KALVALLAEGCGEAVVNVAEPVATQSSATLLRGVCASPGSAFGQVVQVTDPELVITEQGT Sbjct: 241 KALVALLAEGCGEAVVNVAEPVATQSSATLLRGVCASPGSAFGQVVQVTDPELVITEQGT 300 Query: 301 GGATERAALTRGLLAANEALQVLQDKAAGSAQAEIFRAHQELLEDPTLLEHAHRLLGEGK 360 GGATERAALTRGLLAANEALQVLQDKAAGSAQAEIFRAHQELLEDPTLLEHAHRLLGEGK Sbjct: 301 GGATERAALTRGLLAANEALQVLQDKAAGSAQAEIFRAHQELLEDPTLLEHAHRLLGEGK 360 Query: 361 SAAFAWNSATLATVTLFQGLGNALIAERAADLADVGQRVLKLILGIQDSAWDLPERAILI 420 SAAFAWNSATLATVTLFQGLGNALIAERAADLADVGQRVLKLILGIQDSAWDLPERAILI Sbjct: 361 SAAFAWNSATLATVTLFQGLGNALIAERAADLADVGQRVLKLILGIQDSAWDLPERAILI 420 Query: 421 AEQLTPSQTASLDTRKVLGFVTVAGGATSHVAILARALGLPAICGVPAQVLALANGKQVL 480 AEQLTPSQTASLDTRKVLGFVTVAGGATSHVAILARALGLPAICGVPAQVLALANGKQVL Sbjct: 421 AEQLTPSQTASLDTRKVLGFVTVAGGATSHVAILARALGLPAICGVPAQVLALANGKQVL 480 Query: 481 LDADKGELHLEPNLAEIEQLEAARKHQVLRHQRDVAQASLPATTRDGHHVEVTANVASLQ 540 LDADKGELHLEPNLAEIEQLEAARKHQVLRHQRDVAQASLPATTRDGHHVEVTANVASLQ Sbjct: 481 LDADKGELHLEPNLAEIEQLEAARKHQVLRHQRDVAQASLPATTRDGHHVEVTANVASLQ 540 Query: 541 EVEHALTLGGEGVGLLRSEFLYLDRNRAPSPEEQAGTYTAIARALGTERNLVVRTLDVGG 600 EVEHALTLGGEGVGLLRSEFLYLDRNRAPSPEEQAGTYTAIARALGTERNLVVRTLDVGG Sbjct: 541 EVEHALTLGGEGVGLLRSEFLYLDRNRAPSPEEQAGTYTAIARALGTERNLVVRTLDVGG 600 Query: 601 DKPLAYVPMDAETNPFLGLRGIRLCLERPQLLREQFRAILASAGFARLHIMLPMVSLLSE 660 DKPLAYVPMDAETNPFLGLRGIRLCLERPQLLREQFRAILASAGFARLHIMLPMVSLLSE Sbjct: 601 DKPLAYVPMDAETNPFLGLRGIRLCLERPQLLREQFRAILASAGFARLHIMLPMVSLLSE 660 Query: 661 LHLARKILEEEALALGLTELPKLGIMIEVPSAALMADVFAPHVDFFSIGTNDLTQYTLAM 720 LHLARKILEEEALALGLTELPKLGIMIEVPSAALMADVFAPHVDFFSIGTNDLTQYTLAM Sbjct: 661 LHLARKILEEEALALGLTELPKLGIMIEVPSAALMADVFAPHVDFFSIGTNDLTQYTLAM 720 Query: 721 DRDHPRLANQADSFHPAVLRLIATTVKAAHAHGKWVGVCGALASEALAVPVLIGLGVDEL 780 DRDHPRLANQADSFHPAVLRLIATTVKAAHAHGKWVGVCGALASEALAVPVLIGLGVDEL Sbjct: 721 DRDHPRLANQADSFHPAVLRLIATTVKAAHAHGKWVGVCGALASEALAVPVLIGLGVDEL 780 Query: 781 SVSVPLIPTIKATVRELDLADCQIIARQVLGLEEAAEVREALRQYHAATVESSPVVEH 838 SVSVPLIPTIKATVRELDLADCQIIARQVLGLEEAAEVREALRQYHAATVESSPVVEH Sbjct: 781 SVSVPLIPTIKATVRELDLADCQIIARQVLGLEEAAEVREALRQYHAATVESSPVVEH 838 Lambda K H 0.318 0.133 0.371 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: 2066 Number of extensions: 57 Number of successful extensions: 1 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: 838 Length of database: 838 Length adjustment: 42 Effective length of query: 796 Effective length of database: 796 Effective search space: 633616 Effective search space used: 633616 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 56 (26.2 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