Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate WP_010538521.1 KCY_RS0118745 polyamine ABC transporter ATP-binding protein
Query= TCDB::Q97UF2 (371 letters) >NCBI__GCF_000226135.1:WP_010538521.1 Length = 461 Score = 181 bits (458), Expect = 5e-50 Identities = 118/354 (33%), Positives = 185/354 (52%), Gaps = 20/354 (5%) Query: 4 IRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPTSGY 63 I V ++SK F + A+D+V++ + G +LGPSG GKTT LRLIAG + + G Sbjct: 8 IEVSHVSKFFG----DKTALDDVTLNVKKGEFVTILGPSGCGKTTLLRLIAGFQTASEGE 63 Query: 64 IYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIENKV 123 I + ++ P KR + VFQ +AL+P++ V+DNIAF LKL K PK I KV Sbjct: 64 IRISGKEITQT-----PPHKRPVNTVFQKYALFPHLNVYDNIAFGLKLKKTPKQTIGKKV 118 Query: 124 KEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRESARA 183 K + +G++ R LSGGQ QR AIARA+V +P+VLLLDEP + LD ++R+ + Sbjct: 119 KAALKMVGMTDYEYRDVDSLSGGQQQRVAIARAIVNEPEVLLLDEPLAALDLKMRKDMQM 178 Query: 184 LVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIARLT 243 ++++ + +T + V+HD + +++ V+ GK QIGTP +IY P +A Sbjct: 179 ELKEMHKSLGITFVYVTHDQEEALTLSDTIVVMSEGKIQQIGTPIDIYNEPINSFVADFI 238 Query: 244 GEINLIQAKIIENNAI-IANLKVPLNNMELKGQSNIVIGLRPDDLTLSDTLLDKYIDMGI 302 GE N++ +I + + + + + + + +RP+DL + + D G+ Sbjct: 239 GESNILNGTMIHDKLVRFCGTEFECVDEGFGENTPVDVVIRPEDLYIF-PVSDMAQLTGV 297 Query: 303 VKVKLVSYGAGIFKIVVSPIT--DENIDIIVDAEEPLETGIETHLLAKPNKVKI 354 V+ IFK V +T + +V E G E LL KP + I Sbjct: 298 VQ-------TSIFKGVHYEMTVLCGGYEFLVQDYHHFEVGAEVGLLVKPFDIHI 344 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: 348 Number of extensions: 16 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: 461 Length adjustment: 31 Effective length of query: 340 Effective length of database: 430 Effective search space: 146200 Effective search space used: 146200 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: 50 (23.9 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