Align ABC transporter for Glycerol, ATPase component 2 (characterized)
to candidate AO356_05180 AO356_05180 sugar ABC transporter ATP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_792 (358 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_05180 Length = 386 Score = 196 bits (497), Expect = 1e-54 Identities = 114/327 (34%), Positives = 186/327 (56%), Gaps = 13/327 (3%) Query: 27 LKMEFEDGGAYALLGPSGCGKTTMLNIMSGLLVPSHGKVLFDGRDVTRASPQERNIAQVF 86 +++ +DG L+GPSGCGK+T++N ++GL + G ++ +DV+ SP++R+IA VF Sbjct: 24 IELSIKDGEFLILVGPSGCGKSTLMNCIAGLETITGGAIMIGDQDVSGMSPKDRDIAMVF 83 Query: 87 QFPVIYDTMTVAENLAFPLRNRKVPEGQIKQRVGVIAEMLEMSGQLNQRAAGLAADAKQK 146 Q +Y TM+V EN+ F L+ RK+ + I + V +A++L++ LN++ L+ +Q+ Sbjct: 84 QSYALYPTMSVRENIEFGLKIRKMNQSAIDEEVNRVAKLLQIEHLLNRKPGQLSGGQQQR 143 Query: 147 ISLGRGLVRADVAAVLFDEPLTVIDPHLKWQLRRKLKQIHHELKLTLIYVTHDQVEALTF 206 +++GR L R LFDEPL+ +D L+ ++R ++K +H LK T +YVTHDQ+EA+T Sbjct: 144 VAMGRALARRP-KIYLFDEPLSNLDAKLRVEMRTEMKLMHQRLKTTTVYVTHDQIEAMTL 202 Query: 207 ADQVVVMTRGKAVQVGSADALFERPAHTFVGHFIGSPGMNFLP---AHRDGENLSVAGH- 262 D+V VM G Q G+ ++ PA+ FV FIGSP MNF+P +DG L++ Sbjct: 203 GDKVAVMKDGIIQQFGTPKDIYTNPANLFVASFIGSPPMNFIPLRLQRKDGRLLALLDSG 262 Query: 263 --RLASPVG---RALPAGALQVGIRPEYLALA--QPQQAGALPGTVVQVQDIGTYQMLTA 315 R P+G L + +G+RPE + LA +P + V + G ++ Sbjct: 263 QARCELPMGMQDAGLEDREVILGMRPEQIMLAGSEPNGLPTIRAEVQVTEPTGPDTLVFV 322 Query: 316 KVGEHTVKARFTPETRLPSSGDTAWLQ 342 + + V R P+ P G+T LQ Sbjct: 323 SLNDTKVCCRLAPDV-APQVGETLTLQ 348 Lambda K H 0.320 0.136 0.395 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: 329 Number of extensions: 18 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: 358 Length of database: 386 Length adjustment: 30 Effective length of query: 328 Effective length of database: 356 Effective search space: 116768 Effective search space used: 116768 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