Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate WP_017547633.1 C792_RS0101285 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= TCDB::Q97UF2 (371 letters) >NCBI__GCF_000330705.1:WP_017547633.1 Length = 387 Score = 219 bits (559), Expect = 8e-62 Identities = 130/375 (34%), Positives = 207/375 (55%), Gaps = 17/375 (4%) Query: 1 MTTIRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPT 60 M +++E++ K + G V + ++ I G ++GPSG GK+T LR+IAGLE+ T Sbjct: 1 MAEMKLESIKKTYDNGPA---VVHDFNLEIYDGEFIVLVGPSGCGKSTTLRMIAGLEDIT 57 Query: 61 SGYIYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIE 120 G Y ++ R + P+ R IAMVFQN+ALYP+M+V+DN+AF LKL KVPK +I+ Sbjct: 58 DGDFY-----IAGKRMNDVEPKNRDIAMVFQNYALYPHMSVYDNMAFGLKLRKVPKPEIK 112 Query: 121 NKVKEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRES 180 +V++ +E LGL+ L+R PK LSGGQ QR A+ RA+V++ V L+DEP SNLDA++R Sbjct: 113 ERVEKAAEILGLTDFLDRKPKALSGGQRQRVALGRAIVREANVFLMDEPLSNLDAKLRVQ 172 Query: 181 ARALVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYPATDLIA 240 RA + K+ + K TT+ V+HD + +A + V+ G Q+GTP E+Y++P +A Sbjct: 173 MRAEITKLHKRLKTTTIYVTHDQTEALTMATRIVVMNEGDIMQVGTPKEVYDFPENVFVA 232 Query: 241 RLTGE--INLIQAKIIENNAIIANLKVPLNNMELK-----GQSN--IVIGLRPDDLTLSD 291 + G +N+ A+I + +I N ++ + + + G N + G+RP+D+ Sbjct: 233 QFIGSPAMNIFDAEIKDGKLVIGNTEITIPEAKRRMLIDEGYDNKALKFGIRPEDIREEA 292 Query: 292 TLLDKYIDMGIVKVKLVSYGAGIFKIVVSPITDENIDIIVDAEEPLETGIETHLLAKPNK 351 ++ + VS G ++ S + + VDA L G NK Sbjct: 293 VFVESALASAFKAEVKVSELLGSEIMLYSELEGQEFISRVDARNELNPGDVVKFAFDMNK 352 Query: 352 VKIFDLNGSNLITSK 366 FD+ I++K Sbjct: 353 GHFFDMYSGERISTK 367 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: 328 Number of extensions: 10 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: 387 Length adjustment: 30 Effective length of query: 341 Effective length of database: 357 Effective search space: 121737 Effective search space used: 121737 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