Align ATPase (characterized, see rationale)
to candidate PfGW456L13_446 Cystine ABC transporter, ATP-binding protein
Query= uniprot:Q31RN8 (261 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_446 Length = 251 Score = 228 bits (581), Expect = 9e-65 Identities = 124/247 (50%), Positives = 163/247 (65%), Gaps = 7/247 (2%) Query: 21 MIYAEGVEKWYGNQFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRGEIW 80 MI E + K + Q L G+ L V+ GEVV ++GPSGSGK+TFLR LN LE G I Sbjct: 1 MIVVEKLTKQFKGQI-VLNGIDLEVKEGEVVAIIGPSGSGKTTFLRCLNFLEEPTSGRIK 59 Query: 81 I------EGHRLSHDRRDIATIRQEVGMVFQQFNLFPHLTVLQNLMLAPVQVRRWPVAQA 134 + L+ + + +RQ VG VFQ FNLFPH T L+N++ P+ V++ P A A Sbjct: 60 VGDIEVDTSRPLNQQQSLVRRLRQHVGFVFQNFNLFPHRTALENVIEGPIVVKKTPHADA 119 Query: 135 EATARQLLERVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVR 194 A ++LL +V +A + D YP +LSGGQQQRVAIARALAM+P ++LFDEPTSALDPE+V Sbjct: 120 VALGKKLLAKVGLAGKEDAYPRRLSGGQQQRVAIARALAMEPEVILFDEPTSALDPELVG 179 Query: 195 EVLDVMRDLASEGMTMLVATHEVGFAREVADRVVLMADGQIVEEAPPDRFFTAPQSDRAK 254 EVL +R LA E TM++ THE+GFAR+VA+RVV G IVE+ F P+ +R K Sbjct: 180 EVLATIRGLAEEKRTMVIVTHEMGFARDVANRVVFFDKGVIVEQGEAKALFANPKEERTK 239 Query: 255 QFLAQIL 261 QFL++ L Sbjct: 240 QFLSKFL 246 Lambda K H 0.321 0.134 0.387 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: 208 Number of extensions: 8 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: 261 Length of database: 251 Length adjustment: 24 Effective length of query: 237 Effective length of database: 227 Effective search space: 53799 Effective search space used: 53799 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 (21.9 bits) S2: 47 (22.7 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