Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate 3607946 Dshi_1354 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= uniprot:A3DE72 (327 letters) >FitnessBrowser__Dino:3607946 Length = 416 Score = 124 bits (312), Expect = 3e-33 Identities = 75/232 (32%), Positives = 117/232 (50%), Gaps = 21/232 (9%) Query: 95 FWFALRNTAIYTVVVTFATFALGIILAMLVNREFKGRGIVRTALLMPWVVPSYVVGMTWG 154 FW L T YTV T G+ A+L+N+ F+G+GI+R L P+V P V TW Sbjct: 190 FWGVLGVTMFYTVFGTLGALLFGLFAALLLNKSFRGQGILRGLYLFPYVAPVIAVAFTWV 249 Query: 155 FLWRQDSGLINIILCDI------LHILPEKPYWLVGSNQIWAIIIPTIWRGLPLSMILML 208 L+ SG N +L + ++ ++P L+ + + IWR PLS + +L Sbjct: 250 TLFDPFSGSANALLIQMGVTNEAINFFGQRPLALI------MVTVFEIWRYFPLSFLFIL 303 Query: 209 AGLQSISPDYYEAADIDGANGWQKFWHITLPLLKPILAINVMFSLISNIYSFNIVSMMFG 268 A +QSI D YEAAD+DGA+ +QKFW+++LP+L IL++ + I F+ + ++ G Sbjct: 304 ARMQSIDTDMYEAADMDGASPFQKFWYLSLPMLVGILSVLFLLRFIWTFNKFDDIFLLTG 363 Query: 269 NGAGIPGEWGDLLMTYIQRNTFQMWRFGPGAAALMIVMFFVLGIVALWYTLF 320 AG L + F + G GAA ++ + G + L+ LF Sbjct: 364 GNAGT-----RTLTVNVYEQAFAVSNIGAGAAVAVV----IFGCLLLFSVLF 406 Lambda K H 0.330 0.145 0.468 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: 413 Number of extensions: 20 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 327 Length of database: 416 Length adjustment: 30 Effective length of query: 297 Effective length of database: 386 Effective search space: 114642 Effective search space used: 114642 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (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