Align ABC transporter (characterized, see rationale)
to candidate AZOBR_RS25335 AZOBR_RS25335 putative ABC transporter (ATP-binding protein)
Query= uniprot:A0A166QFW2 (381 letters) >FitnessBrowser__azobra:AZOBR_RS25335 Length = 365 Score = 252 bits (643), Expect = 1e-71 Identities = 143/320 (44%), Positives = 198/320 (61%), Gaps = 13/320 (4%) Query: 1 MIKLKLDNVNKQLG-GMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGD 59 ++ L LD + K+ G L +SLE+A GE + VGPSGCGK+T LRLIAGL GG Sbjct: 7 LVPLALDRLAKRYGTAPPALAALSLEVAGGELLGLVGPSGCGKTTALRLIAGLTPASGGR 66 Query: 60 LLIDGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKTDKTSLRERVLKTAQ 119 +L+ GR + L RG+G+VFQ+YAL+PHM+ DN++FGL++ R + Sbjct: 67 VLVGGRDITALPAHARGIGLVFQNYALFPHMTAADNVAFGLRMRGLPAAERHARTAEALA 126 Query: 120 ILQLDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARL 179 +++L L RKP+ LSGGQ+QRVA+ RA+A P++LL DEPLSNLDA LR ++ EI L Sbjct: 127 MVRLSHLGGRKPRALSGGQQQRVALARALAIRPNLLLLDEPLSNLDAGLRAELLAEIRTL 186 Query: 180 HDRLGSTMIYVTHDQVEAMTLADKIVVLNGGRVEQVGSPRELYERPASRFVAGFLGSPRM 239 RLG T ++VTHDQ EA+ + D+I VL GR+EQVG+PRE+++RPAS FVAGF+G R Sbjct: 187 QRRLGITALFVTHDQGEALAVCDRIAVLRDGRLEQVGTPREVHDRPASGFVAGFVG--RT 244 Query: 240 NFLSARLQTPGETSLVDTLVWGITSLPFDSSNLAAGTPLSLGIRPEHVSLKAADGTAGV- 298 N + A G + TL+ + P AG P+ L +RP + + AA G G+ Sbjct: 245 NRIPAERLAGGALRVGGTLLPALADGP-------AG-PVDLFVRPHRIRVGAAGGAGGLP 296 Query: 299 -VVTAVEYLGSETYVHLETG 317 V+ +LG + LE G Sbjct: 297 AVLRGTAFLGDRIALSLEAG 316 Lambda K H 0.320 0.137 0.394 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: 402 Number of extensions: 12 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: 381 Length of database: 365 Length adjustment: 30 Effective length of query: 351 Effective length of database: 335 Effective search space: 117585 Effective search space used: 117585 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