Align ABC transporter for L-Histidine, periplasmic substrate-binding component 1 (characterized)
to candidate 206398 DVU0966 amino acid ABC transporter, periplasmic amino acid-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_2555 (249 letters) >MicrobesOnline__882:206398 Length = 272 Score = 107 bits (268), Expect = 2e-28 Identities = 78/261 (29%), Positives = 123/261 (47%), Gaps = 23/261 (8%) Query: 8 LLASLAAAAFCTTGAQAQD---------------NVLRVGTDATFPPMEFVE-NGKRTGF 51 LLA++ AA A A D LRVG DA + P E + NG GF Sbjct: 6 LLAAMMMAALLAAPAMAADIELAKKSTLNEIMARGELRVGFDAGYLPFEMTDKNGNYVGF 65 Query: 52 DIELVEAIAKTMGKQVEWVDIDFKGLIPGLISKRFDMAVSAIYITDERKKVVDFTDSYYA 111 DI++ + +A+ MG + V+ DF G+IP L+S +FD+ +S + +T ER ++F D Y Sbjct: 66 DIDIAKEMARAMGVKFVPVNTDFDGMIPALLSDKFDIIISGMTVTQERNLKINFADPYIV 125 Query: 112 GGLVVMV--KADNKAINKLADLDGKKVSV--QVGTKSVSYLTEKFPKVQRVEVEKNQEMF 167 G V++ K + K + DL+ + +V ++GT PK + +K + Sbjct: 126 VGQTVLLSKKLEGK-VKSWKDLNSPEYTVVSRLGTTGEEAAKRMLPKAKFKSFDKEADGA 184 Query: 168 NLVDIGRADAAVTGKP--AAFQYVRTRPGLRVLDEQLTTEEYGMALRKDTPELTKAVNGA 225 V GRADA V P F + + + LD+ T E G ++K P+ +N Sbjct: 185 LEVVNGRADAWVYDMPFNVVFMAEQGKDKVVHLDKPFTYEPLGFGIKKGDPDFLNFLNNF 244 Query: 226 ITKLKADGTYAAIVKKWFSNS 246 + ++K DG Y I KW ++ Sbjct: 245 MRQIKNDGRYDRIYDKWMRST 265 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: 164 Number of extensions: 10 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: 272 Length adjustment: 24 Effective length of query: 225 Effective length of database: 248 Effective search space: 55800 Effective search space used: 55800 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