Align Polar amino acid ABC transporter, inner membrane subunit; Flags: Precursor (characterized, see rationale)
to candidate AO353_11990 AO353_11990 ABC transporter permease
Query= uniprot:B2TBJ7 (240 letters) >FitnessBrowser__pseudo3_N2E3:AO353_11990 Length = 231 Score = 176 bits (445), Expect = 5e-49 Identities = 94/233 (40%), Positives = 143/233 (61%), Gaps = 6/233 (2%) Query: 4 IQMLGFGPEGWGGVLLLAALMTVALTLAALAVGAVFGALVAAAKLSRFRTLRVIGDIYTT 63 I + GFGP L ALMTV L L+AL +G V G L A AK S ++ L+ +G Y+T Sbjct: 3 IDLYGFGP-----ALAAGALMTVKLALSALCLGLVLGLLGALAKTSPYKPLQWLGGTYST 57 Query: 64 VFRGVPELLVIYLFYFGGSTLVTSVGQLFGAEGFVGVPPFVVGALAVGMISGAYQAEVYR 123 + RG+PELL + L YFG L+ ++G+ FG + + F G +A+G+ GAY EV+R Sbjct: 58 LVRGIPELLWVLLIYFGTVNLMRALGEFFGNPD-LALNAFAAGVIALGLCFGAYATEVFR 116 Query: 124 SAVLAVSRGELEAARSIGMPTLTMARRILIPQVLRFALPGIGNVWQLSLKDSALISVTGL 183 A+LA+ +G EA ++G+ L + R+++PQ+ R ALPG+GN++ + +KD+AL+SV GL Sbjct: 117 GAILAIPKGHREAGVALGLSKLRIFTRLILPQMWRIALPGLGNLFMILMKDTALVSVIGL 176 Query: 184 AELLRTSQVAAGSTHQYFTFFVVGGALYLIMTSISNRVFNRAEAHVGRSFKRN 236 E++R +Q T Q FTF++V +YL +T ++ + E R F RN Sbjct: 177 EEIMRHAQNGVTMTKQPFTFYMVAAFMYLGLTILAMTGMHLLEKRAARGFARN 229 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: 126 Number of extensions: 4 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: 240 Length of database: 231 Length adjustment: 23 Effective length of query: 217 Effective length of database: 208 Effective search space: 45136 Effective search space used: 45136 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 Apr 09 2024. 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