Align ABC transporter for L-Histidine, periplasmic substrate-binding component 1 (characterized)
to candidate PP_0227 PP_0227 periplasmic cystine-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_2555 (249 letters) >FitnessBrowser__Putida:PP_0227 Length = 264 Score = 142 bits (358), Expect = 7e-39 Identities = 88/249 (35%), Positives = 133/249 (53%), Gaps = 6/249 (2%) Query: 7 LLLASLAAAAFCTTGAQA--QDNVLRVGTDATFPPMEFV-ENGKRTGFDIELVEAIAKTM 63 LL A L + AF + + V+ VG + T+PP F ENGK TGF++EL E +AK + Sbjct: 16 LLGAGLLSQAFAGEQLKTIQEKGVINVGLEGTYPPFSFQDENGKLTGFEVELSELLAKEL 75 Query: 64 GKQVEWVDIDFKGLIPGLISKRFDMAVSAIYITDERKKVVDFTDSYYAGGLVVMV---KA 120 G + + + G++ L SKR D+ V+ + I++ERKK DF++ Y G+ ++ KA Sbjct: 76 GVKAKIQPTKWDGILAALESKRLDVVVNQVTISEERKKKYDFSEPYTVSGIQALILKKKA 135 Query: 121 DNKAINKLADLDGKKVSVQVGTKSVSYLTEKFPKVQRVEVEKNQEMFNLVDIGRADAAVT 180 + I DL GKKV V +GT ++ + P+ E + F + GR DA + Sbjct: 136 EQLNIKGAQDLAGKKVGVGLGTNYEQWVKKDVPQADVRTYEDDPSKFADLRNGRIDAILI 195 Query: 181 GKPAAFQYVRTRPGLRVLDEQLTTEEYGMALRKDTPELTKAVNGAITKLKADGTYAAIVK 240 + AA +Y + + + + E G+ALRK PEL A+N AI KLKADGT A + + Sbjct: 196 DRLAALEYAQKAKDTELAGDAFSRLESGVALRKGEPELLAAINKAIDKLKADGTLAKLSE 255 Query: 241 KWFSNSAAK 249 K+F K Sbjct: 256 KYFGADVTK 264 Lambda K H 0.317 0.133 0.369 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: 152 Number of extensions: 6 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: 249 Length of database: 264 Length adjustment: 24 Effective length of query: 225 Effective length of database: 240 Effective search space: 54000 Effective search space used: 54000 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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