Align Polar amino acid ABC transporter, inner membrane subunit; Flags: Precursor (characterized, see rationale)
to candidate PfGW456L13_384 Histidine ABC transporter, permease protein HisQ (TC 3.A.1.3.1)
Query= uniprot:B2TBJ7 (240 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_384 Length = 242 Score = 178 bits (451), Expect = 1e-49 Identities = 90/226 (39%), Positives = 145/226 (64%), Gaps = 1/226 (0%) Query: 1 MALIQMLGFGPEGWGGVLLLAALMTVALTLAALAVGAVFGALVAAAKLSRFRTLRVIGDI 60 + ++ + GF +G+G +LL + MTV L+ L V G + A+AKLS+ LRV Sbjct: 6 LMILGLSGFSLKGFGPLLLQGSWMTVKLSFLCLLVSVGLGLIGASAKLSKSALLRVPAQA 65 Query: 61 YTTVFRGVPELLVIYLFYFGGSTLVTSVGQLFGAEGFVGVPPFVVGALAVGMISGAYQAE 120 YTT+ RGVP+L+++ L ++ T +TS+ + G + ++ + PF G + +G I GAY E Sbjct: 66 YTTLIRGVPDLVLMLLIFYSLQTWLTSLTEALGWD-YIEINPFSAGVITLGFIYGAYFTE 124 Query: 121 VYRSAVLAVSRGELEAARSIGMPTLTMARRILIPQVLRFALPGIGNVWQLSLKDSALISV 180 +R A+LAV RG++EAA + G+ R ++ PQ++RFALPGIGN W + LK +AL+S+ Sbjct: 125 TFRGAILAVPRGQMEAATAYGLTRAQRFRLVVFPQMMRFALPGIGNNWMVILKATALVSI 184 Query: 181 TGLAELLRTSQVAAGSTHQYFTFFVVGGALYLIMTSISNRVFNRAE 226 GLA+L++ +Q A S++Q F F ++ +YL++T++SN V R E Sbjct: 185 IGLADLVKVAQDAGKSSYQLFFFLILAALIYLVITTVSNYVLRRME 230 Lambda K H 0.327 0.141 0.403 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: 125 Number of extensions: 6 Number of successful extensions: 2 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: 240 Length of database: 242 Length adjustment: 23 Effective length of query: 217 Effective length of database: 219 Effective search space: 47523 Effective search space used: 47523 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: 46 (22.3 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