Align GtsB (GLcF), component of Glucose porter, GtsABCD (characterized)
to candidate YP_426349.1 Rru_A1261 binding-protein dependent transport system inner membrane protein
Query= TCDB::Q88P37 (302 letters) >NCBI__GCF_000013085.1:YP_426349.1 Length = 298 Score = 122 bits (305), Expect = 1e-32 Identities = 91/295 (30%), Positives = 144/295 (48%), Gaps = 15/295 (5%) Query: 12 PLDALQR------WLPKLVLAPSMFIVLVGFYGYILWTFVLSFTTSTFL-PTYK-WAGLA 63 P+ AL+R W L P + ++ +LW S T + PTY + GL Sbjct: 8 PMTALERADRRFGWFLTL---PGVLMLAATIAFPLLWAVATSLFDFTLIAPTYDTFVGLD 64 Query: 64 QYARLFDNDRWWVASKNLLLFGGLFIAISLAIGVLLAVLLDQRIRREGFIRTIYLYPMAL 123 YA N + AS + F + I AIG L+A++L+ R + I L P+ + Sbjct: 65 NYALALGNTEFLHASWLTVGFVVAVVLIEFAIGFLIALMLNGVRRGKPIYYAILLCPLLI 124 Query: 124 SMIVTGTAWKWLLNPGMGLDKLLRDWGWEGFR-LDWLIDPDRVVYCLVIAAVWQASGFIM 182 + +V G W+ +L+P +G+ G G ++WL D + LV +W F++ Sbjct: 125 NPVVVGLVWRMVLHPTLGVANYAL--GLIGLSPVNWLGDVTVAFWTLVGVDIWHQVSFMI 182 Query: 183 AMFLAGLRGVDPSIIRAAQMDGASLPRIYWTVVLPSLRPVFFSALMILSHIAIKSFDLVA 242 + LAGL + AA++DGAS+ + +W + LP +R V L+I A+K++DLV Sbjct: 183 VLLLAGLSALPAEPYEAARVDGASVFQRFWHITLPLMRRVILVTLLIRMIFAVKTYDLVY 242 Query: 243 AMTAGGPGYSSDLPAMFMYSFTFSRGQMGMGSASAILMLGAILAILVPYLYSELR 297 MT GGPG ++DL + +Y F +G +A A L+L +L I YLY +R Sbjct: 243 IMTRGGPGTATDLVSYSIYRTAFVGLNLGQATAMAGLLLIPVLGI-TAYLYRLMR 296 Lambda K H 0.330 0.142 0.455 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: 238 Number of extensions: 10 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: 302 Length of database: 298 Length adjustment: 27 Effective length of query: 275 Effective length of database: 271 Effective search space: 74525 Effective search space used: 74525 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: 48 (23.1 bits)
This GapMind analysis is from Sep 24 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