Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate AZOBR_RS00070 AZOBR_RS00070 glycerol-3-phosphate transporter permease
Query= uniprot:A3DHA3 (284 letters) >FitnessBrowser__azobra:AZOBR_RS00070 Length = 294 Score = 136 bits (343), Expect = 5e-37 Identities = 88/278 (31%), Positives = 149/278 (53%), Gaps = 10/278 (3%) Query: 10 YLFSSPYLAGFLIFFAIPSAM----SVYYCFTRGVGSFEFAGLDNFKSVIASNSYRLAVK 65 YL +P +A LIFF P+A SV+ G+ S +F GL+NF++V++ +Y VK Sbjct: 14 YLLLAPQVAVTLIFFIWPAAQALWQSVHLQDAFGLRS-QFVGLENFQAVLSDPNYLETVK 72 Query: 66 NTLIFNSVSVPVIMIVSLL-LAMLLNKALRGARYFRMFFVLPLVIPVASIILVWQITFN- 123 T++F S SV V+ + S L LA++ + +R A ++ + P + A ++W FN Sbjct: 73 TTIVF-SASVTVLSLASALGLAVMADSKIRAASAYKTLLIWPYALAPAVAAVLWMFIFNP 131 Query: 124 EFGVLNNLLNHFGIAGVEWLNSKWSIAVLVLLYVWKNCGYNIILFTAGLNSIPKDYYDAA 183 + G+L LN+ G A LN ++ +++L WK YN I F AGL +IP+ +AA Sbjct: 132 DIGILGRALNNLGYAWDYRLNDGQALTMVILAASWKQVSYNFIFFLAGLQAIPRSVLEAA 191 Query: 184 SIDGAGGFKCFTSITLPLLVPTIFFVFIISIINS-FKVFREAYLLCGNYP-PLNMYMLQH 241 SIDGAG + F +IT PLL PT FF+ +++I+ + F+ F + L P ++ Sbjct: 192 SIDGAGAVRRFWTITFPLLSPTTFFLLVVNIVYAFFETFGTIHALTHGGPGKATETLIFR 251 Query: 242 FMNNNFNNLNYQRLSTASLLMELFIVAIVFLMYKIEGR 279 + N + S S+++ + ++A+ + ++ R Sbjct: 252 VYQDGVVNHDLGGSSAQSVILMVIVIALTAIQFRFVER 289 Lambda K H 0.331 0.144 0.444 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: 209 Number of extensions: 7 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: 284 Length of database: 294 Length adjustment: 26 Effective length of query: 258 Effective length of database: 268 Effective search space: 69144 Effective search space used: 69144 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 bits) S2: 48 (23.1 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