Align AraV, component of Arabinose, fructose, xylose porter (characterized)
to candidate WP_008537164.1 HMPREF9454_RS00035 methionine ABC transporter ATP-binding protein
Query= TCDB::Q97UF2 (371 letters) >NCBI__GCF_000245775.1:WP_008537164.1 Length = 353 Score = 162 bits (409), Expect = 2e-44 Identities = 86/231 (37%), Positives = 141/231 (61%) Query: 4 IRVENLSKIFKKGKTEVKAVDNVSITIDSGMAFGVLGPSGHGKTTFLRLIAGLEEPTSGY 63 I+++N+ K + V A+ ++++ I G +G++G SG GK+T +R I LE PTSG Sbjct: 2 IKLKNIVKTYDTPNGSVHALKDINLEIKRGEIYGIIGLSGAGKSTLVRCINMLERPTSGN 61 Query: 64 IYFDNEAVSSPRRVMMSPEKRGIAMVFQNWALYPNMTVFDNIAFPLKLAKVPKDKIENKV 123 + + + +++ + ++ I M+FQ++ L TV+DNIAFPLKLA K++I+ KV Sbjct: 62 VIVNGKDLTTMTESQLREARKDIGMIFQHFNLLSTSTVYDNIAFPLKLAGKSKEEIKAKV 121 Query: 124 KEVSEELGLSGVLNRYPKELSGGQMQRTAIARALVKDPKVLLLDEPFSNLDAQIRESARA 183 + + + +GL ++YP +LSGGQ QR IARAL D KVLL DE S LD Q ++ Sbjct: 122 EPLLKLVGLENKAHQYPSQLSGGQKQRVGIARALANDTKVLLCDEATSALDPQTTKAILE 181 Query: 184 LVRKIQRERKLTTLIVSHDPADIFAIANKAGVIVNGKFAQIGTPTEIYEYP 234 L+R I ++ +LT ++++H+ I + +K V+ +G A+ GT EI+ P Sbjct: 182 LIRDINKKLQLTVVVITHEMQVIKDLCDKVAVLDHGVIAENGTVLEIFTNP 232 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: 304 Number of extensions: 11 Number of successful extensions: 1 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: 353 Length adjustment: 29 Effective length of query: 342 Effective length of database: 324 Effective search space: 110808 Effective search space used: 110808 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 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