Align Acetate permease ActP-2/ActP2/ActP3 (characterized)
to candidate WP_011338330.1 RSPH17029_RS11235 cation acetate symporter
Query= TCDB::D5APM1 (578 letters) >NCBI__GCF_000015985.1:WP_011338330.1 Length = 605 Score = 151 bits (381), Expect = 8e-41 Identities = 138/515 (26%), Positives = 218/515 (42%), Gaps = 85/515 (16%) Query: 56 ITKWAAGRTKSAADFYTAGGGITGFQNGLAIAGDYMSAASFLGISAAVMLQ---GYDGLI 112 I WA R S A+FY AG G+ NG+A D+MSAASF+ ++ + L GY Sbjct: 21 IAIWA--RAGSTAEFYAAGQGVHPVMNGMATGADWMSAASFISMAGIIALAPAGGYTQSA 78 Query: 113 YSIGFLVGWPILTFLMAERLRNLGKFTFADVAAFPFAQTPVRVFAAMSTLVVVAFYLIAQ 172 + +G+ G+ +L L+A LR GKFT + F R+ A + +++ Y+I Q Sbjct: 79 FLMGWTGGYVLLALLLAPYLRKFGKFTVPEFIGDRFYSGGARLLAVVCLIIISITYVIGQ 138 Query: 173 MVGAGQLIKLLFGLEYLYAVIVVGILMMVYVLFGGMTATTWVQIIKACLLLGGASFMALM 232 M G G + + + ++ Y +FGGM T+ Q+ + +L+ + A+ Sbjct: 139 MRGVGVTFGRFLEISTDMGLYIGAAIVFAYAVFGGMKGITYTQVAQYVVLIIAYTIPAIF 198 Query: 233 VMVHYGFSLESLFADSVKVKTDLALAAGKTPEEAAAAG----ISIMGPGTFVKDPISAIS 288 + + +L F + + D A A G ++A A ++ +G + D S ++ Sbjct: 199 ISL----ALTGAFLPQLGLIGDYAPAGG---DQAFLAKLDQVVTELGFTAYTADTPSMLN 251 Query: 289 ---FGMALMFGTAGLPHILMRFFTVPSAKEARKSVMWATVWIGYFYMLTFIIGFGAIVYV 345 F M+LM GTAGLPH+++RFFTVP +AR S WA V+I Y + +G A + + Sbjct: 252 MFLFTMSLMIGTAGLPHVIIRFFTVPKVADARSSAGWALVFIALLYTVAPAVGSMARLNL 311 Query: 346 LTN--PGLV-------------------------SYDAKGALTLVGGNN----------- 367 T PG V +++ G L + N Sbjct: 312 TTTMWPGAVTGNALDADAISVEAIQTDPRLNWVKTWEQTGLLVMEDLNGDGKIQYYNDKN 371 Query: 368 --MAAIHLAQAVGGNIFLGF-----------ISAVAFATILAVVAGLTLSGASAVS---- 410 MA + + GN I+A+ I V AG + S + Sbjct: 372 PAMAEVAAERGWAGNEVTKIDNDIMVLANPEIAALPGWVIALVAAGALAAALSTAAGLLL 431 Query: 411 -------HDLYSTVFKNGKADSASELRVSRITTICLGIVAVVLGLAFEKQNIAF-MVSLA 462 HDL N EL +RI+ G +A+ L A +V+LA Sbjct: 432 AISSAISHDLIKGSI-NPNISEKGELLAARIS--MTGAIAIATWLGLNPPGFAAQVVALA 488 Query: 463 FAIAASANFPVLFMSLLWKGMTTRGAVIGGSLGLI 497 F +AA+ FP L M + K + GA++G +GLI Sbjct: 489 FGLAAATIFPALMMGIFSKRVNKEGAILGMLVGLI 523 Lambda K H 0.326 0.138 0.405 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: 986 Number of extensions: 57 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 578 Length of database: 605 Length adjustment: 37 Effective length of query: 541 Effective length of database: 568 Effective search space: 307288 Effective search space used: 307288 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Apr 10 2024. 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