Align ABC transporter for D-mannitol and D-mannose, ATPase component (characterized)
to candidate Ac3H11_1610 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= reanno::pseudo3_N2E3:AO353_25895 (367 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1610 Length = 362 Score = 238 bits (607), Expect = 2e-67 Identities = 148/366 (40%), Positives = 215/366 (58%), Gaps = 16/366 (4%) Query: 1 MAHLKIKNLQKGFEGFSIIKGIDLEVNDREFVVFVGPSGCGKSTLLRLIAGLEEVTAGTI 60 M+ L++ ++ K + ++ ++L V EFV +GPSGCGK+T L+++AG E VT+G I Sbjct: 1 MSFLQLTDVTKFYGSTCAVQSMNLSVEKGEFVSLLGPSGCGKTTTLQMVAGFEAVTSGRI 60 Query: 61 ELDGRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVNKAEVEKKVNEAARI 120 EL GRDIT R L +VFQ+YAL+PHM+V N+SF L++ V KAE + +V +A + Sbjct: 61 ELAGRDITHAKANTRGLGIVFQSYALFPHMTVADNVSFGLEMRKVPKAERKDRVAQALGL 120 Query: 121 LELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARLH 180 + L R P++LSGGQRQRVA+ RA+V P + L DEPLSNLDA LR +M+ EL ++ Sbjct: 121 VHLEKHAGRYPRELSGGQRQRVALARALVIEPPVLLLDEPLSNLDAKLREEMQFELRQIQ 180 Query: 181 KELQATMIYVTHDQVEAMTLADKVVVLNGGRIEQVGSPLELYHQPANLFVAGFLGTPKMG 240 +++ T + VTHDQ EAM+++D+VVV+ GR Q+ P +Y P F++ F+G K Sbjct: 181 RKVGTTTVMVTHDQSEAMSISDRVVVMEAGRATQIDHPHRVYEHPRTRFISTFVG--KAN 238 Query: 241 FLKGKVTRVERQNCEVLLDAGTRITLPLSGANLSIGGAVTLGIRPEHLNLALPGDCTLQ- 299 + G+VT + V AG I + + GA G AV L +RPE L L T+Q Sbjct: 239 LVPGQVTTASATHTHV--GAGP-IEVRVEGAQFRPGAAVLLSVRPEKLQLV----PTVQG 291 Query: 300 -VTADVSER--LGSDTFCHVLTASGEALTMRIR-GDLASRYGEQLSLHLDAEHC-HLFDA 354 + +V ER LGS V T G+ + + G A GE+ L +HC L A Sbjct: 292 RIDGEVCERFFLGSQWLYRVGTGMGDLMVLAPNDGRGALEEGERTGLDW-PDHCMRLLPA 350 Query: 355 NGVAVA 360 + A+A Sbjct: 351 DEAALA 356 Lambda K H 0.321 0.137 0.390 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: 331 Number of extensions: 15 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: 367 Length of database: 362 Length adjustment: 29 Effective length of query: 338 Effective length of database: 333 Effective search space: 112554 Effective search space used: 112554 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