Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate RR42_RS00200 RR42_RS00200 ABC transporter permease
Query= uniprot:Q1MCU1 (463 letters) >FitnessBrowser__Cup4G11:RR42_RS00200 Length = 376 Score = 154 bits (389), Expect = 5e-42 Identities = 95/310 (30%), Positives = 168/310 (54%), Gaps = 26/310 (8%) Query: 142 ILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLSSYFGLSFWVLLPLSGIFAAL 201 +L+Y GL + G +G+ + AF+ +G+Y+ A+++ + G+ +++ +SG+ AAL Sbjct: 88 VLLYTTACLGLTLQFGFSGVANFAGAAFFGIGSYATAVMAMHTGIPHLLIIVISGVIAAL 147 Query: 202 WGVILGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTDVTKGTFGISSIPKATLFGIPFDA 261 G +L PVLR RG Y A+VT+AFG + + I DV G G+ +P T+FG A Sbjct: 148 VGSMLITPVLRTRGHYAALVTIAFGILFK-TFIEVNDVLGGPQGLQ-VPGMTIFGY---A 202 Query: 262 TAGGFAKLFHLPISSAYYKIFLFYLILALCMLTA-YVTIR-LRRMPIGRAWEALREDEIA 319 GF ++ ++ Y +++L + + T++ L R +G + + +R DE A Sbjct: 203 LNDGFT------VAGVDVSFYVSYALISLGICAGVFATVKALERSWVGLSMDVVRTDETA 256 Query: 320 CRSLGINTVTTKLTAFATGAMFAGFAGSFFAARQGFVSPESFVFLESAVILAIVVLGGMG 379 + G++ K+ AF G FAG AGS + GFV+P +F F +S ++L+IV+LGG+G Sbjct: 257 AATFGLHIARWKVVAFMLGNFFAGIAGSMYGMITGFVAPNNFTFSDSLLMLSIVILGGLG 316 Query: 380 SLTGIAIAAIVMVGGTELLREMSFLKLIFGPDFTPELYRMLIFGLAMVVVMLFKPRGFVG 439 + G+ AAI+++ L ++ F+ + YR L + ++ ++LF+P G + Sbjct: 317 NAVGLIPAAIIVL---VLPEKLQFI----------QEYRFLFYAALVIAILLFRPDGLLP 363 Query: 440 SREPTAFLRE 449 + F RE Sbjct: 364 RKTRLFFGRE 373 Lambda K H 0.330 0.145 0.432 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: 505 Number of extensions: 23 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: 463 Length of database: 376 Length adjustment: 31 Effective length of query: 432 Effective length of database: 345 Effective search space: 149040 Effective search space used: 149040 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: 50 (23.9 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