Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate Pf1N1B4_409 L-arabinose transport system permease protein (TC 3.A.1.2.2)
Query= uniprot:D8IZC8 (344 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_409 Length = 322 Score = 171 bits (432), Expect = 3e-47 Identities = 94/281 (33%), Positives = 154/281 (54%), Gaps = 2/281 (0%) Query: 59 NFASAENTMNILRQVAINLVLAAGMTFVILTAGIDLSVGSVLAVSAVLGMQVSLGAAPGW 118 NF S N + ++ + A M + + + DLSVGSV+A + V+ V + Sbjct: 43 NFLSPLNMRGLGLAISTTGIAACTMLYCLASGHFDLSVGSVIACAGVVAAVVMRDTDSVF 102 Query: 119 -AIPMFIFSGLVMGMVNGAMVALLNINAFVVTLGTMTAFRGAAYLLADGTTVLNNDIPSF 177 + + GL++G++NG ++A L +NA + TL TM RG AY+ A+G V + F Sbjct: 103 LGVSAALVMGLIVGLINGIVIAKLRVNALITTLATMQIVRGLAYIFANGKAVGVSQEQFF 162 Query: 178 EWIGNGDFLHVPWLIWVAVAVVLLSWVILRKTVLGMHIYAIGGNLQAARLTGIRVGLVLL 237 + GNG VP I + + L +L T G + AIGGN +AA L G+ V Sbjct: 163 VF-GNGQLFGVPVPILITIVCFLFFGWLLNYTTYGRNTMAIGGNQEAALLAGVNVDRTKT 221 Query: 238 FVYSISGLFSGLAGAMSASRLYGANGNWGSGYELDAIAAVVLGGTSLMGGVGSIWGTVVG 297 ++++ G+ LAG + ASR+ G G+EL I+A VLGG SL GG+G I + G Sbjct: 222 LIFAVHGVIGALAGVILASRMTSGQPMIGQGFELTVISACVLGGVSLSGGIGMIRHVIAG 281 Query: 298 ALIIGVMNNGLTILGLSSFWQYVAKGAVIVLAVILDKWRQK 338 LI+ ++ N + + + +F+QYV +G++++LAV++D+ +Q+ Sbjct: 282 VLILAIIENAMNLKNIDTFYQYVIRGSILLLAVVIDRLKQR 322 Lambda K H 0.324 0.138 0.417 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: 273 Number of extensions: 18 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: 344 Length of database: 322 Length adjustment: 28 Effective length of query: 316 Effective length of database: 294 Effective search space: 92904 Effective search space used: 92904 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 49 (23.5 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