Align ABC transporter for Glycerol, ATPase component 2 (characterized)
to candidate AZOBR_RS25595 AZOBR_RS25595 sugar ABC transporter ATP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_792 (358 letters) >FitnessBrowser__azobra:AZOBR_RS25595 Length = 358 Score = 187 bits (476), Expect = 3e-52 Identities = 111/288 (38%), Positives = 169/288 (58%), Gaps = 11/288 (3%) Query: 29 MEFEDGGAYALLGPSGCGKTTMLNIMSGLLVPSHGKVLFDGRDVTRASPQERNIAQVFQF 88 +E DG A +GPSGCGK+T+L +++GL PS G + G+ V P R IA VFQ Sbjct: 24 LEVADGEFVAFVGPSGCGKSTLLRLIAGLEEPSGGDLSIGGQRVNDRPPAARGIAMVFQS 83 Query: 89 PVIYDTMTVAENLAFPLRNRKVPEGQIKQRVGVIAEMLEMSGQLNQRAAGLAADAKQKIS 148 +Y MT +N+AF L + +G I +RV A +L++ L+++ L+ +Q+++ Sbjct: 84 YALYPHMTAYDNMAFGLTLSRTDKGTIAERVRAAARLLQIEDLLDRKPRDLSGGQRQRVA 143 Query: 149 LGRGLVRADVAAVLFDEPLTVIDPHLKWQLRRKLKQIHHELKLTLIYVTHDQVEALTFAD 208 +GR +VR + LFDEPL+ +D L+ Q+R ++ ++ +L+ T+IYVTHDQVEA+T AD Sbjct: 144 IGRAIVR-EPQVFLFDEPLSNLDAGLRVQMRLEIAKLKADLRATMIYVTHDQVEAMTLAD 202 Query: 209 QVVVMTRGKAVQVGSADALFERPAHTFVGHFIGSPGMNFLPAHRDG-ENLSV-----AGH 262 ++VV+ G+ Q G+ L+ RP + FV FIGSP MNFL +G + SV G Sbjct: 203 RIVVLNAGRVEQAGTPLELYHRPRNRFVAGFIGSPAMNFLDVVSEGLTDGSVRVWLPGGV 262 Query: 263 RLASPVGRALPAGA--LQVGIRPEYLALAQPQQAGALPGTVVQVQDIG 308 L V A PA L +G+RPE++ LA L T++ V+ +G Sbjct: 263 PLDIAVDGAAPAAGTPLTLGVRPEHVGLA--DGGAGLLATILAVERLG 308 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: 322 Number of extensions: 17 Number of successful extensions: 3 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: 358 Length adjustment: 29 Effective length of query: 329 Effective length of database: 329 Effective search space: 108241 Effective search space used: 108241 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