Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate RR42_RS29445 RR42_RS29445 ABC transporter permease
Query= uniprot:Q1MCU1 (463 letters) >FitnessBrowser__Cup4G11:RR42_RS29445 Length = 358 Score = 168 bits (426), Expect = 2e-46 Identities = 101/304 (33%), Positives = 160/304 (52%), Gaps = 34/304 (11%) Query: 142 ILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLSSYFGLSFWVLLPLSGIFAAL 201 +LIY + GL ++ G GLL +G+ AF VGAY+ A L+S+ G+ F L + +AL Sbjct: 50 VLIYAIAGLGLMVLSGYTGLLSIGHAAFLGVGAYTQAWLTSH-GVPFVPALLAAAALSAL 108 Query: 202 WGVILGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTDVTKGTFGISSIPKATLFGIPFDA 261 GV++G P LR++G YLAI TLAFG I+ +L W VT G G+ + L+G D Sbjct: 109 TGVVVGLPALRVKGIYLAIATLAFGLIVEEILARWESVTGGNAGLP-VAAPQLWGYVLDG 167 Query: 262 TAGGFAKLFHLPISSAYYKIFLFYLILALCMLTAYVTIRLRRMPIGRAWEALREDEIACR 321 + +YL LA+C+L + L R GRA+ A+R+ EI+ + Sbjct: 168 P------------------VAFYYLSLAVCLLATLAVLNLLRSATGRAFIAIRDSEISAQ 209 Query: 322 SLGINTVTTKLTAFATGAMFAGFAGSFFAARQGFVSPESFVFLESAVILAIVVLGGMGSL 381 S+GI+ K +FA A G AG+ +A + ++SPE F +S +L +VV+GG+GS+ Sbjct: 210 SMGIHLARYKTLSFALSAALVGIAGALYAHKLRYISPEQFGIAQSIDLLLLVVVGGLGSV 269 Query: 382 TGIAIAAIVMVGGTELLREMSFLKLIFGPDFTPEL------YRMLIFGLAMVVVMLFKPR 435 G + AI ++ ++ ++ D P + L++GL ++ +LF+P Sbjct: 270 HGAFLGAIFLIVMPQM--------IVLAKDLLPPAIGQASGMQALVYGLVLMAFVLFEPM 321 Query: 436 GFVG 439 G G Sbjct: 322 GLYG 325 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: 482 Number of extensions: 29 Number of successful extensions: 5 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: 463 Length of database: 358 Length adjustment: 31 Effective length of query: 432 Effective length of database: 327 Effective search space: 141264 Effective search space used: 141264 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