Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate GFF1647 PGA1_c16700 binding protein-dependent transport system, inner membrane component
Query= uniprot:C8WUR0 (321 letters) >FitnessBrowser__Phaeo:GFF1647 Length = 316 Score = 133 bits (334), Expect = 6e-36 Identities = 101/322 (31%), Positives = 160/322 (49%), Gaps = 48/322 (14%) Query: 12 GRERAKRRVDWV----AYGYLSPALVTICVLSILPIFYTIYISFTNFNQMHFLSYQFVGL 67 G A+R + W + YLSP ++ I + ++P+ I SF + ++ + +VG Sbjct: 17 GGTGARRSLYWQYMVEPFLYLSPMILLIGSVMLIPLIVGISYSFQSIELLNPFATGWVGF 76 Query: 68 KNYEELLNPHD---PLSNLFLPTFIWTLVYALCTTALAYLVGLFLAVLLNNKHMRERTLY 124 +NYE+L + L N F TF W++ + + +GL LA+LLN + ++ L+ Sbjct: 77 ENYEKLWSDRKFWIALENTFFWTF-WSIFFQ-------FFLGLGLAMLLNTQFFGKK-LF 127 Query: 125 RTLLIVPWAVPNLISMLAWQGLLNDQYGQINALL---------HGVFGLPRIPWLTSALW 175 + L+ +PWAVP +S L W L N G I L + + G P + A+W Sbjct: 128 QALVFLPWAVPTFLSALTWAWLFNPVIGPIPHWLAALGVLSEPYNILGDPDL-----AIW 182 Query: 176 ARIAVIMVNVWAGFPYMMTVCLGALQSIPTDQYEAAEIDGANWWQVFRYVTMPSVWRISL 235 I N+W G P+ L ALQSIP + YEAAEIDGA WQ F +T+P + + Sbjct: 183 GPITA---NIWFGVPFFAITLLAALQSIPGELYEAAEIDGATPWQSFTKITLPFLAPMIA 239 Query: 236 PLLIPSFSYNFNNFNASYLLTGGGPPNSNNPFLGQTDILATAAYKMTLTFNRYDLG--AT 293 ++ + N + +++TGGGP NS T IL+T Y T F + D G +T Sbjct: 240 ITVMLRTIWIANFADLIFVMTGGGPANS-------TQILST--YIFTTAFRKLDFGYAST 290 Query: 294 ISVLLFILV----ALISWVQMR 311 I+V L I++ ++ W++ R Sbjct: 291 IAVALLIILLAYAVILLWMRKR 312 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: 369 Number of extensions: 20 Number of successful extensions: 4 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: 321 Length of database: 316 Length adjustment: 27 Effective length of query: 294 Effective length of database: 289 Effective search space: 84966 Effective search space used: 84966 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: 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