Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate PP_5179 PP_5179 spermidine/putrescine ABC transporter - ATP binding subunit
Query= reanno::acidovorax_3H11:Ac3H11_791 (363 letters) >FitnessBrowser__Putida:PP_5179 Length = 380 Score = 159 bits (401), Expect = 2e-43 Identities = 101/307 (32%), Positives = 162/307 (52%), Gaps = 10/307 (3%) Query: 5 LDSISKKVGAQTWLYDMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVTVDGK 64 +D ++KK + D+SL ++ G + LLG + +GK++L+R++AG + P+ GR+ +DG Sbjct: 25 IDRVTKKFDETVAVDDVSLEIRKGEIFALLGGSGSGKSTLLRMLAGFERPSEGRIFLDGV 84 Query: 65 DVTGMPVRDRNVAMVYQQFINYPSMKVAANIASPLKL--RGEKNIDARVREIASRLHIDM 122 D+T MP +R + M++Q + +P M VA NIA L+ + IDARV E+ +H+ Sbjct: 85 DITDMPPYERPINMMFQSYALFPHMTVAQNIAFGLQQDKMPKAEIDARVAEMLKLVHMTQ 144 Query: 123 FLDRYPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELTQLFAAGQS 182 + R P +LSGGQ+QRVALAR+LAK L+LLDEP+ LD KLR +++ EL ++ Sbjct: 145 YAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRSQMQLELVEIIERVGV 204 Query: 183 TVVYATTEPGEALLLGGYTAVLDEGQLLQYGPTAEVFHAPNSLRVARAFSDPPMNLMAAS 242 T V T + EA+ + A++ G + Q G +++ P S V + +NL Sbjct: 205 TCVMVTHDQEEAMTMAQRIAIMHLGWIAQIGSPVDIYETPTSRLVCEFIGN--VNLFEGD 262 Query: 243 AT--AQGVRLQGGAELTLPLPQGAATAAGLTVGVRASALRVHARPGDVSVAGVVELAEIS 300 A+G + EL + G G+T V + RP + V E + Sbjct: 263 VVDDAEGYAIIASPELERKIYVG----HGITTSVEDKHITYALRPEKMLVTTQQPTCEHN 318 Query: 301 GSDTFVH 307 S +H Sbjct: 319 WSRGKIH 325 Lambda K H 0.318 0.133 0.375 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: 246 Number of extensions: 11 Number of successful extensions: 2 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: 363 Length of database: 380 Length adjustment: 30 Effective length of query: 333 Effective length of database: 350 Effective search space: 116550 Effective search space used: 116550 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