Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate Ac3H11_1610 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= uniprot:D8IPI1 (406 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1610 Length = 362 Score = 217 bits (552), Expect = 5e-61 Identities = 115/279 (41%), Positives = 173/279 (62%), Gaps = 6/279 (2%) Query: 13 YAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGTLRIGGTVVNDLP 72 + G + ++L + GEFV LLGPSGCGK+T L+M+AG E ++ G + + G + Sbjct: 12 FYGSTCAVQSMNLSVEKGEFVSLLGPSGCGKTTTLQMVAGFEAVTSGRIELAGRDITHAK 71 Query: 73 ARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAALLNLEALLERKP 132 A R + +VFQ+YAL+PHM+V DN++FGL K P AE RV + L++LE R P Sbjct: 72 ANTRGLGIVFQSYALFPHMTVADNVSFGLEMRKVPKAERKDRVAQALGLVHLEKHAGRYP 131 Query: 133 RAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRLHQRLRTTTVYVT 192 R +SGGQ+QR A+ARA++ P V L DEPLSNLDAKLR +++ +++++ +++ TTTV VT Sbjct: 132 RELSGGQRQRVALARALVIEPPVLLLDEPLSNLDAKLREEMQFELRQIQRKVGTTTVMVT 191 Query: 193 HDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAMNFLSGTVQRQDG 252 HDQ EAM+++DRV++M+ GR Q P +Y +PR F + F+G N + G V Sbjct: 192 HDQSEAMSISDRVVVMEAGRATQIDHPHRVYEHPRTRFISTFVG--KANLVPGQVTTASA 249 Query: 253 -QLFIETAHQRWALTGERFSRLRHAMAVKLAVRPDHVRI 290 + + G +F R AV L+VRP+ +++ Sbjct: 250 THTHVGAGPIEVRVEGAQF---RPGAAVLLSVRPEKLQL 285 Lambda K H 0.321 0.137 0.403 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: 328 Number of extensions: 8 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: 406 Length of database: 362 Length adjustment: 30 Effective length of query: 376 Effective length of database: 332 Effective search space: 124832 Effective search space used: 124832 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: 50 (23.9 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