Align ABC transporter related (characterized, see rationale)
to candidate AZOBR_RS06625 AZOBR_RS06625 heme ABC transporter ATP-binding protein
Query= uniprot:A0KWY5 (499 letters) >FitnessBrowser__azobra:AZOBR_RS06625 Length = 511 Score = 251 bits (640), Expect = 6e-71 Identities = 169/509 (33%), Positives = 269/509 (52%), Gaps = 22/509 (4%) Query: 5 LELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILFL 64 LE + ++K + A DVSL + G +H ++GENGAGKST++ ++ G D G IL Sbjct: 8 LETRGVNKWFGANHANRDVSLAVPKGTIHGVIGENGAGKSTIMSIVYGYLPADGGTILVD 67 Query: 65 GEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADARAV 124 G P +P DA AGI V+Q LV TV +N+ LG E G + A AR Sbjct: 68 GRPVAVRSPRDALAAGIGMVHQHFMLVDPFTVLENVLLGAE----GGVTLAAGMARARTE 123 Query: 125 LTQ----FKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLF 180 LT+ + L++D+ P+ + + QQ + I + + A +L+LDEPT L +E LF Sbjct: 124 LTRLARDYGLEVDLDRPVGELPVGAQQRVEILKALYRGADILILDEPTGVLTPQETDHLF 183 Query: 181 GILNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRS 240 IL L+ +G +V ITH L ++ +++D +TV+R GQ + TA + +L E M+GR Sbjct: 184 RILRALREQGKTVVIITHKLREIMELTDNVTVMRRGQVVANVATARTSREELAELMVGRK 243 Query: 241 LQEQLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEV 300 + + V+K E L + D + ++ + LTV G+ VG+AG+ G+G+SE+ Sbjct: 244 VLLR-VEKVPATPGPAVLEVSGLCVRDGAGVERVKGIGLTVRAGEIVGIAGVSGNGQSEL 302 Query: 301 CNAVFGLDLVDSGSIHLAGQKLNLSQPVDAISA------GIALCPEDRKIDGIIGPLSIR 354 A+ G+ GS+ L G++L + D +A G+ PEDR+ G++ + Sbjct: 303 LEALAGMRPPAEGSVRLRGEELTATP--DRFTARGLRALGVGHVPEDRQRVGLVTGFEAQ 360 Query: 355 ENIILALQARIGWWRYLSNTRQQ--EIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILA 412 E IL Q + L R+ + +D + D P SGGNQQK++LA Sbjct: 361 ECAILGHQGDPAFNGRLLMDRRALFDRCASEMDAYDVRPRDPRLPAANFSGGNQQKIVLA 420 Query: 413 RWLAIEPILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVV 472 R + P LL++ +PTRG+DIGA I + + L D+G ++L+ S ELDE+ A S++++V Sbjct: 421 REMERNPDLLLVGQPTRGVDIGAIEFIHRRLVALRDQGKAILLVSVELDEIRALSDRILV 480 Query: 473 LRDRYAVRELSGAELTSQH---VMQAIAE 498 + D V E++ E + +M +AE Sbjct: 481 MFDGRLVGEVAPGEADERRLGLMMAGVAE 509 Lambda K H 0.319 0.136 0.377 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: 597 Number of extensions: 37 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: 499 Length of database: 511 Length adjustment: 34 Effective length of query: 465 Effective length of database: 477 Effective search space: 221805 Effective search space used: 221805 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