Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate Ac3H11_2058 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= BRENDA::Q70HW1 (384 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2058 Length = 360 Score = 234 bits (597), Expect = 3e-66 Identities = 145/363 (39%), Positives = 207/363 (57%), Gaps = 24/363 (6%) Query: 2 ARVLLEHIYKTYPGQTEPT--VKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITE 59 A ++ +I K Y + VK + ++ T +GPSGCGKTTTLRMIAGLE T Sbjct: 6 AGIVFRNITKRYGTDSSAALAVKGISFEVPRGTLTTILGPSGCGKTTTLRMIAGLESPTS 65 Query: 60 GNLYIGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEA 119 G ++IG + V + P R+++M+FQ+YAL+PHM V +N+ +GL++ PK + + EA Sbjct: 66 GEIFIGGKDVTTLGPAQRNVSMMFQSYALFPHMNVVENVMYGLRMSGQPKEQARAKAVEA 125 Query: 120 AKILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIR 179 + + + DR P LSGGQ+QRVAL RA+V EP+V L DEPLSNLDA+LR +MR EIR Sbjct: 126 LRGVGLVGFDDRLPSELSGGQQQRVALARALVLEPEVLLFDEPLSNLDARLRREMREEIR 185 Query: 180 KLHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSP 239 L QRL TV YVTHDQ EAM + D+I+VM G+I Q +P+ +Y P + FVAGF+G Sbjct: 186 ALQQRLSLTVAYVTHDQAEAMAVSDQIIVMNQGLIAQKGSPRALYETPHSEFVAGFMGE- 244 Query: 240 AMNFIRGEIVQDGDAFYFRAPSISLRLPEGRYGVLKASGAIGKPVVLGVRPEDLHDEEVF 299 AM F V D D P + R V SG PV + VRPE Sbjct: 245 AMLF---PAVADADGTVALGPLVL------RPRVAVKSG----PVKVAVRPEAWR----- 286 Query: 300 MTTYPDSVLQMQVEVVEHMGS--EVYLHTSIGPNTIVARVNPRHVYHVGSSVKLAIDLNK 357 +T + +L ++ ++G+ E T++G + V + V VG V+L + ++ Sbjct: 287 ITRQGEGLLPARLAKSAYLGAVHEYTFETALG-SIFVVSSDLDDVLAVGDDVQLGLGVHG 345 Query: 358 IHI 360 + + Sbjct: 346 VSV 348 Lambda K H 0.321 0.138 0.395 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: 325 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: 384 Length of database: 360 Length adjustment: 30 Effective length of query: 354 Effective length of database: 330 Effective search space: 116820 Effective search space used: 116820 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: 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