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:C8WUR0 (321 letters) >FitnessBrowser__Dino:3607946 Length = 416 Score = 99.0 bits (245), Expect = 2e-25 Identities = 72/224 (32%), Positives = 106/224 (47%), Gaps = 13/224 (5%) Query: 91 TLVYALCTTALAYLVGLFLAVLLNNKHMRERTLYRTLLIVPWAVPNLISMLAWQGLLNDQ 150 T+ Y + T A L GLF A+LLN K R + + R L + P+ P + W L + Sbjct: 197 TMFYTVFGTLGALLFGLFAALLLN-KSFRGQGILRGLYLFPYVAPVIAVAFTWVTLFDPF 255 Query: 151 YGQINALL--HGVFGLPRIPWLTSALWARIAVIMVNVWAGFPYMMTVCLGALQSIPTDQY 208 G NALL GV I + A I V + +W FP L +QSI TD Y Sbjct: 256 SGSANALLIQMGVTN-EAINFFGQRPLALIMVTVFEIWRYFPLSFLFILARMQSIDTDMY 314 Query: 209 EAAEIDGANWWQVFRYVTMPSVWRISLPLLIPSFSYNFNNFNASYLLTGGGPPNSNNPFL 268 EAA++DGA+ +Q F Y+++P + I L + F + FN F+ +LLTGG Sbjct: 315 EAADMDGASPFQKFWYLSLPMLVGILSVLFLLRFIWTFNKFDDIFLLTGGN--------- 365 Query: 269 GQTDILATAAYKMTLTFNRYDLGATISVLLFILVALISWVQMRY 312 T L Y+ + GA ++V++F + L S + R+ Sbjct: 366 AGTRTLTVNVYEQAFAVSNIGAGAAVAVVIFGCLLLFSVLFFRF 409 Score = 30.4 bits (67), Expect = 8e-05 Identities = 14/40 (35%), Positives = 24/40 (60%) Query: 12 GRERAKRRVDWVAYGYLSPALVTICVLSILPIFYTIYISF 51 GR RR +A+G L P ++++ ++ ILP+ +ISF Sbjct: 12 GRGALHRREARLAWGLLLPTVISVSLVVILPLLAIFWISF 51 Lambda K H 0.327 0.140 0.451 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: 347 Number of extensions: 25 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 321 Length of database: 416 Length adjustment: 30 Effective length of query: 291 Effective length of database: 386 Effective search space: 112326 Effective search space used: 112326 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 (21.7 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