Align ABC-type sugar transport system, ATP-binding protein; EC 3.6.3.17 (characterized, see rationale)
to candidate AZOBR_RS06625 AZOBR_RS06625 heme ABC transporter ATP-binding protein
Query= uniprot:A0A0C4Y5F6 (540 letters) >FitnessBrowser__azobra:AZOBR_RS06625 Length = 511 Score = 275 bits (703), Expect = 3e-78 Identities = 191/518 (36%), Positives = 269/518 (51%), Gaps = 22/518 (4%) Query: 12 PLLALRNICKTFPGVRALRKVELTAYAGEVHALMGENGAGKSTLMKILSGAYTADPGGEC 71 P L R + K F A R V L G +H ++GENGAGKST+M I+ G AD GG Sbjct: 6 PALETRGVNKWFGANHANRDVSLAVPKGTIHGVIGENGAGKSTIMSIVYGYLPAD-GGTI 64 Query: 72 HIDGQRVQIDGPQSARDLGVAVIYQELSLAPNLSVAENIYLGRALQRRGLVARGDMVRAC 131 +DG+ V + P+ A G+ +++Q L +V EN+ LG G+ M RA Sbjct: 65 LVDGRPVAVRSPRDALAAGIGMVHQHFMLVDPFTVLENVLLGA---EGGVTLAAGMARA- 120 Query: 132 APTLARLGADFSPAAN----VASLSIAQRQLVEIARAVHFEARILVMDEPTTPLSTHETD 187 L RL D+ + V L + +Q VEI +A++ A IL++DEPT L+ ETD Sbjct: 121 RTELTRLARDYGLEVDLDRPVGELPVGAQQRVEILKALYRGADILILDEPTGVLTPQETD 180 Query: 188 RLFALIRQLRGEGMAILYISHRMAEIDELADRVTVLRDGCFVGTLDRAHLSQAALVKMMV 247 LF ++R LR +G ++ I+H++ EI EL D VTV+R G V + A S+ L ++MV Sbjct: 181 HLFRILRALREQGKTVVIITHKLREIMELTDNVTVMRRGQVVANVATARTSREELAELMV 240 Query: 248 GRDLSGFYTK---THGQAVEREVMLSVRDVADGRRVKGCSFDLRAGEVLGLAGLVGAGRT 304 GR + K T G AV L VRD A RVKG +RAGE++G+AG+ G G++ Sbjct: 241 GRKVLLRVEKVPATPGPAVLEVSGLCVRDGAGVERVKGIGLTVRAGEIVGIAGVSGNGQS 300 Query: 305 ELARLVFGADARTRGEVRIANPAGSGGLVTLPAGGPRQAIDAGIAYLTEDRKLQGLFLDQ 364 EL + G G VR+ + A G R G+ ++ EDR+ GL Sbjct: 301 ELLEALAGMRPPAEGSVRLRGEELTATPDRFTARGLRAL---GVGHVPEDRQRVGLVTGF 357 Query: 365 SVHENINLIVAARDALGLGRL--NRTAARRRTTEAIDTLGIRVAHAQVNVGALSGGNQQK 422 E ++ D GRL +R A R +D +R ++ SGGNQQK Sbjct: 358 EAQE-CAILGHQGDPAFNGRLLMDRRALFDRCASEMDAYDVRPRDPRLPAANFSGGNQQK 416 Query: 423 VMLSRLLEIQPRVLILDEPTRGVDIGAKSEIYRLINALAQSGVAILMISSELPEVVGLCD 482 ++L+R +E P +L++ +PTRGVDIGA I+R + AL G AIL++S EL E+ L D Sbjct: 417 IVLAREMERNPDLLLVGQPTRGVDIGAIEFIHRRLVALRDQGKAILLVSVELDEIRALSD 476 Query: 483 RVLVMREGTLAGEVRPAGSAAETQERIIALATGAAAAA 520 R+LVM +G L GEV P E ER + L A A Sbjct: 477 RILVMFDGRLVGEVAP----GEADERRLGLMMAGVAEA 510 Lambda K H 0.320 0.136 0.382 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: 697 Number of extensions: 46 Number of successful extensions: 9 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: 540 Length of database: 511 Length adjustment: 35 Effective length of query: 505 Effective length of database: 476 Effective search space: 240380 Effective search space used: 240380 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: 52 (24.6 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