Align L-arabinose ABC transporter, permease protein AraH (characterized)
to candidate WP_013090553.1 BC1002_RS13335 L-arabinose ABC transporter permease AraH
Query= CharProtDB::CH_014278 (328 letters) >NCBI__GCF_000092885.1:WP_013090553.1 Length = 338 Score = 350 bits (899), Expect = e-101 Identities = 180/310 (58%), Positives = 232/310 (74%), Gaps = 3/310 (0%) Query: 20 RIWDQ---YGMLVVFAVLFIACAIFVPNFATFINMKGLGLAISMSGMVACGMLFCLASGD 76 R W Q Y ++V+F V+F+ ++ V +F + NM GL L+IS GMVAC M+FCLAS D Sbjct: 28 RWWQQITEYSLIVIFIVMFVTMSLTVDHFFSIENMLGLALSISQIGMVACTMMFCLASRD 87 Query: 77 FDLSVASVIACAGVTTAVVINLTESLWIGVAAGLLLGVLCGLVNGFVIAKLKINALITTL 136 FDLSV S +A AGV A+V+N T S I + A + G + G VNG VIA L+INALITTL Sbjct: 88 FDLSVGSTVAFAGVLCAMVLNATNSTVIAIIAAVAAGGVIGFVNGAVIAYLRINALITTL 147 Query: 137 ATMQIVRGLAYIISDGKAVGIEDESFFALGYANWFGLPAPIWLTVACLIIFGLLLNKTTF 196 ATM+IVRGL +I+S G+AVG+ ++F ALG +FG+ PIW+T+ C I+FG++LN+T + Sbjct: 148 ATMEIVRGLGFIVSHGQAVGVSSDTFIALGGLTFFGVSLPIWVTLICFIVFGVMLNQTVY 207 Query: 197 GRNTLAIGGNEEAARLAGVPVVRTKIIIFVLSGLVSAIAGIILASRMTSGQPMTSIGYEL 256 GRNTLAIGGN EA+RLAG+ V RT++ IF++ G V+A+AG+ILASR+TSGQP + G+EL Sbjct: 208 GRNTLAIGGNPEASRLAGINVERTRVYIFLIQGAVTALAGVILASRITSGQPNAAEGFEL 267 Query: 257 IVISACVLGGVSLKGGIGKISYVVAGILILGTVENAMNLLNISPFAQYVVRGLILLAAVI 316 VISACVLGGVSL GG IS VV G+LI+GTVEN MNLLNI F QY+VRG ILLAAV+ Sbjct: 268 NVISACVLGGVSLLGGRATISGVVIGVLIMGTVENVMNLLNIDAFYQYLVRGAILLAAVL 327 Query: 317 FDRYKQKAKR 326 D+ K + R Sbjct: 328 LDQLKNRGSR 337 Lambda K H 0.327 0.141 0.414 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: 367 Number of extensions: 20 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: 328 Length of database: 338 Length adjustment: 28 Effective length of query: 300 Effective length of database: 310 Effective search space: 93000 Effective search space used: 93000 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: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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