Align PotG aka B0855, component of Putrescine porter (characterized)
to candidate AZOBR_RS08840 AZOBR_RS08840 ABC transporter ATP-binding protein
Query= TCDB::P31134 (377 letters) >FitnessBrowser__azobra:AZOBR_RS08840 Length = 387 Score = 406 bits (1043), Expect = e-118 Identities = 213/365 (58%), Positives = 265/365 (72%), Gaps = 6/365 (1%) Query: 18 PLLEIRNLTKSYDGQHAVDDVSLTIYKGEIFALLGASGCGKSTLLRMLAGFEQPSAGQIM 77 P + I +TK++ AVD+VSL+IY+GE FALLG SG GK+TLLRMLAGFE P+ G+I Sbjct: 22 PYVRIEKVTKTFGDFVAVDEVSLSIYRGEFFALLGGSGSGKTTLLRMLAGFETPTEGKIF 81 Query: 78 LDGVDLSQVPPYLRPINMMFQSYALFPHMTVEQNIAFGLKQDKLPKAEIASRVNEMLGLV 137 +DGVD++ +PPY RP+NMMFQSYALFPHM+VEQN+AFGLKQD + KAEI RV +L LV Sbjct: 82 IDGVDMAGIPPYERPVNMMFQSYALFPHMSVEQNVAFGLKQDGVAKAEIKERVGAILDLV 141 Query: 138 HMQEFAKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRDRMQLEVVDILE 197 + +F KRKPHQLSGGQRQRVALARSL KRPKLLLLDEP+GALDK+LR+R Q E+V+I E Sbjct: 142 QLGQFGKRKPHQLSGGQRQRVALARSLVKRPKLLLLDEPLGALDKRLRERTQFELVNIQE 201 Query: 198 RVGVTCVMVTHDQEEAMTMAGRIAIMNRGKFVQIGEPEEIYEHPTTRYSAEFIGSVNVFE 257 ++GVT ++VTHDQEEAMTM+ RIA+MN G Q G P EIYE+P +R+ AEFIGSVN+FE Sbjct: 202 KLGVTFIVVTHDQEEAMTMSSRIAVMNHGVIAQTGTPTEIYEYPQSRFVAEFIGSVNMFE 261 Query: 258 GVLKERQEDGLVLDSPGLVHPLKVDADASVVDNVPVHVALRPEKIMLCEEPPAN------ 311 G + E Q D +++ S L ++ +V V VA+RPEKI L +EPPAN Sbjct: 262 GRVVEDQADHVLIRSEDAGCDLYINHAVAVPAGATVGVAVRPEKIALSKEPPANAATNAD 321 Query: 312 GCNFAVGEVIHIAYLGDLSVYHVRLKSGQMISAQLQNAHRHRKGLPTWGDEVRLCWEVDS 371 G N G V IAYLGD+S+Y V LK+G+ + N R + TW DEV L W + Sbjct: 322 GRNVTSGIVREIAYLGDVSIYLVELKTGKTVRVTAPNVVRRTEMPITWDDEVHLSWRPFA 381 Query: 372 CVVLT 376 VVLT Sbjct: 382 GVVLT 386 Lambda K H 0.321 0.137 0.400 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: 427 Number of extensions: 13 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: 377 Length of database: 387 Length adjustment: 30 Effective length of query: 347 Effective length of database: 357 Effective search space: 123879 Effective search space used: 123879 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