Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate Ac3H11_2066 SN-glycerol-3-phosphate transport ATP-binding protein UgpC (TC 3.A.1.1.3)
Query= uniprot:Q6MNM2 (347 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2066 Length = 355 Score = 318 bits (814), Expect = 2e-91 Identities = 170/355 (47%), Positives = 230/355 (64%), Gaps = 23/355 (6%) Query: 2 AKIQFSNIKKSFGSAD----VLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADS 57 + + + I K FG D VL+ +D+ +APGEFL+LVGPSGCGKSTLL +AGL+ Sbjct: 3 SSLDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTE 62 Query: 58 GTISIDGKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEI 117 G I I GK + + P++RDIAMVFQSYALYP ++VA+N+GF L+++ + E KR++E+ Sbjct: 63 GEIRIGGKNVVGMPPRDRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKRIDEV 122 Query: 118 SELLQIKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIK 177 + +LQI HLLDR+P +LSGGQRQRVA+GRAL+RQ + LFDEPLSNLDA LR +MR EIK Sbjct: 123 AAMLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAEIK 182 Query: 178 RLHHNSKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSP 237 RLH S T +YVTHDQ+EA TLG RIAV+K GV++Q+GTP EIY+RP NT++ATFIGSP Sbjct: 183 RLHQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFIGSP 242 Query: 238 EMNFLEGAV-----------LEKIPWPEARKADQILGIRPDAFALNQGPLGTQEVALGDF 286 MN L GAV L P P + + +LG+RP+ + QE A Sbjct: 243 TMNLLRGAVTGGQFGIQGAALNLAP-PPSSANEVLLGVRPEHLVM-------QETAPWRG 294 Query: 287 QIDISENLGGQQMLHGTLAGNNVRILVDSMDNFSMKQTLPLKIDLTKAHLFDKKT 341 ++ + E G + A +V + D+ + + L + AH FD ++ Sbjct: 295 RVSVVEPTGPDTYVMVDTAAGSVTLRTDAQTRVQPGEHVGLALAPAHAHWFDAQS 349 Lambda K H 0.318 0.136 0.383 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: 342 Number of extensions: 12 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: 347 Length of database: 355 Length adjustment: 29 Effective length of query: 318 Effective length of database: 326 Effective search space: 103668 Effective search space used: 103668 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 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 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