Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate WP_028488909.1 Q394_RS0108480 spermidine/putrescine ABC transporter ATP-binding protein PotA
Query= TCDB::Q97UF2 (371 letters) >NCBI__GCF_000621325.1:WP_028488909.1 Length = 369 Score = 186 bits (473), Expect = 7e-52 Identities = 103/255 (40%), Positives = 159/255 (62%), Gaps = 6/255 (2%) Query: 1 MTTIRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPT 60 MT + LS I K+ ++ + + + ++TI G F +LGPSG GKTT LRLIAG E+P Sbjct: 1 MTRSPILTLSNISKRFASQ-EVLSDFNLTIQDGEFFTILGPSGCGKTTVLRLIAGFEQPN 59 Query: 61 SGYIYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIE 120 G I + + ++ + EKR VFQ++AL+P++TVFDN+AF LK+A V I Sbjct: 60 EGQILLNGDDIAR-----IPAEKRPFNTVFQSYALFPHLTVFDNVAFGLKMAGVDVQDIA 114 Query: 121 NKVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRES 180 +V + + LS R P +LSGGQ QR AIARA+V PK+LLLDE S LD ++R+ Sbjct: 115 VRVADALAIVRLSEFATRKPHQLSGGQKQRVAIARAVVNRPKILLLDESLSALDYKLRQQ 174 Query: 181 ARALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIA 240 + ++++QR+ +T + V+HD + +++++ V+ NG+ Q+GTP EIYE P +A Sbjct: 175 MQLELKQLQRQLGITFVYVTHDQEEALSMSDRILVMHNGQAQQVGTPREIYESPRNLFVA 234 Query: 241 RLTGEINLIQAKIIE 255 + GEIN+ +I++ Sbjct: 235 QFIGEINVFDGEIVQ 249 Lambda K H 0.317 0.136 0.374 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: 284 Number of extensions: 15 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: 371 Length of database: 369 Length adjustment: 30 Effective length of query: 341 Effective length of database: 339 Effective search space: 115599 Effective search space used: 115599 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 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