Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate CCNA_03235 CCNA_03235 spermidine/putrescine transport ATP-binding protein potA
Query= BRENDA::Q97UY8 (353 letters) >FitnessBrowser__Caulo:CCNA_03235 Length = 381 Score = 212 bits (539), Expect = 1e-59 Identities = 119/294 (40%), Positives = 179/294 (60%), Gaps = 19/294 (6%) Query: 4 IIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTGELY 63 I +NV+K F GK+ A+DNV++ + GE F +LGPSG GKTT +R++AG + P+ G + Sbjct: 15 ITFENVTKRF--GKLAAVDNVSLTVNEGEFFALLGPSGCGKTTLLRMLAGFETPTEGRIL 72 Query: 64 FDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKRVEE 123 D + +++ VPP R + MVFQ++A++P++T +N+A+ L + K E RV E Sbjct: 73 IDGQDISN-----VPPNKRPVNMVFQSYAVFPHMTVADNVAYGLKVDNVPKAEREARVAE 127 Query: 124 VAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSARALV 183 +++ + + P +LSGGQ+QRVALARALVK P +LLLDEP S LDA++R+ R + Sbjct: 128 ALELVQLGGLGGRKPDQLSGGQRQRVALARALVKRPRVLLLDEPLSALDAKLREQMRTEL 187 Query: 184 KEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASLIGE 243 +Q ++G+T ++V+HD + A+A R V+ KG L QV P DLY+ P S VA IG+ Sbjct: 188 CTLQEKVGITFIMVTHDQDEALALASRCAVMSKGLLQQVATPSDLYEFPNSRFVADFIGQ 247 Query: 244 INELEGKVTNE---GVVIGSLRFPVSVSSDRAIIG---------IRPEDVKLSK 285 +N EG + + VI S PV + D + G IRPE ++L K Sbjct: 248 VNLFEGVLAVDEPSHAVIKSPDLPVDIFLDHGVTGPRGGTVWAAIRPEKIELHK 301 Lambda K H 0.319 0.139 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: 317 Number of extensions: 9 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: 353 Length of database: 381 Length adjustment: 30 Effective length of query: 323 Effective length of database: 351 Effective search space: 113373 Effective search space used: 113373 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 (21.7 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