Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate GFF3033 PGA1_c30820 putative ABC transporter permease protein
Query= uniprot:A3DE71 (289 letters) >FitnessBrowser__Phaeo:GFF3033 Length = 320 Score = 123 bits (309), Expect = 5e-33 Identities = 75/233 (32%), Positives = 122/233 (52%), Gaps = 20/233 (8%) Query: 63 NYVEVFQKLPFGIYFRNSLIVCSIVMVVALVIATLAGYSLAKYKFPGSGFFGILILATQL 122 NY + F + P Y N +IV + ++ +V+A A Y+LAK KF G L+L L Sbjct: 101 NYSKAFTEAPLLRYLLNGIIVTGSIFLIQVVVALPAAYALAKLKFWGREAVFGLVLFCLL 160 Query: 123 LPGMMFLLPLYLDFVKIKQATGIQLINSIPGLVIVYSAFFVP-----FSIWIIRGFFASI 177 +P LPLY+ K+ GL Y+A VP F I+++R FF ++ Sbjct: 161 IPVHAIALPLYIMLAKL-------------GLTNTYAALVVPWTISVFGIFLMRQFFMTV 207 Query: 178 PGELEEAARIDGCNKFTAFLRVMLPLAVPGIVATAIYIFLTAWDELIFAWVLLKDTK-VT 236 P +L +AAR+DG +F+ RVMLP A+P ++A AI+ + W++ + +++ + + Sbjct: 208 PDDLIDAARMDGMGEFSIVWRVMLPTAIPALLAFAIFSIVAHWNDYFWPRIVVTGNRDLF 267 Query: 237 TIPAGIRGFIAYTTARY-DLLMAAGTIVTIPVLIMFFTMQKKFISGMTAGAVK 288 T P G+R F Y +MA T++ P+++ F QK+FI G+T +K Sbjct: 268 TPPLGLREFKGDGDGSYFGPMMATATVIVTPLIVAFLLAQKRFIEGITLSGMK 320 Lambda K H 0.332 0.145 0.434 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: 247 Number of extensions: 15 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: 289 Length of database: 320 Length adjustment: 27 Effective length of query: 262 Effective length of database: 293 Effective search space: 76766 Effective search space used: 76766 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