Align Glycine betaine/proline betaine transport system ATP-binding protein ProV (characterized)
to candidate WP_000590982.1 HK29_RS06510 amino acid ABC transporter ATP-binding protein
Query= SwissProt::P17328 (400 letters) >NCBI__GCF_000382825.1:WP_000590982.1 Length = 247 Score = 165 bits (417), Expect = 1e-45 Identities = 90/221 (40%), Positives = 140/221 (63%), Gaps = 5/221 (2%) Query: 48 SLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLID--GVDIAKISDAELREVRR 105 +L I++GE+ ++G SG+GKST +R LN L P G + ID VD +KI+ E+ +RR Sbjct: 21 NLDIQKGEVVALIGSSGAGKSTFLRSLNYLETPDSGSIQIDDFSVDFSKITQEEILALRR 80 Query: 106 KKIAMVFQSFALMPHMTVLDNTAFGMELAG-IAAQERREKALDALRQVGLENYAHAYPDE 164 K ++MVFQ F L T LDN G+ + ++ QE + A + L +VGL + + YP Sbjct: 81 K-LSMVFQQFNLFERRTALDNVKEGLVVVKKLSDQEATKIAKEELAKVGLSDRENHYPRH 139 Query: 165 LSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVFISHD 224 LSGG +QRV LARALA+ PD+LL+DE SALDP + E++ + AK +T++ +SHD Sbjct: 140 LSGGQKQRVALARALAMKPDVLLLDEPTSALDPELVGEVEKSIAD-AAKSGQTMILVSHD 198 Query: 225 LDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTFF 265 + ++ D+I + G++++ GTPDEI+++P + + FF Sbjct: 199 MSFVAQVADKILFLDKGKIIESGTPDEIIHHPKEERTKEFF 239 Lambda K H 0.319 0.137 0.378 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: 252 Number of extensions: 10 Number of successful extensions: 4 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: 400 Length of database: 247 Length adjustment: 27 Effective length of query: 373 Effective length of database: 220 Effective search space: 82060 Effective search space used: 82060 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 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