Align ABC transporter for L-Histidine, periplasmic substrate-binding component 1 (characterized)
to candidate HSERO_RS11440 HSERO_RS11440 ABC transporter permease
Query= reanno::acidovorax_3H11:Ac3H11_2555 (249 letters) >FitnessBrowser__HerbieS:HSERO_RS11440 Length = 251 Score = 299 bits (765), Expect = 4e-86 Identities = 148/239 (61%), Positives = 186/239 (77%), Gaps = 1/239 (0%) Query: 9 LASLAAAAFCTTGAQAQDNVLRVGTDATFPPMEFVENGKRTGFDIELVEAIAKTMGKQVE 68 +ASL+ A A V+RVGTDATFPPMEFV++GKRTGFD+EL+EA+AKTMGK+V+ Sbjct: 12 MASLSLLIAAVPAAHANGEVIRVGTDATFPPMEFVKDGKRTGFDVELIEALAKTMGKKVQ 71 Query: 69 WVDIDFKGLIPGLISKRFDMAVSAIYITDERKKVVDFTDSYYAGGLVVMVKADNKAINKL 128 W+DIDFKGLIPGL+S RFD+A SAIY+TDER+KVV+F+D YY GGL V+V+ D+ +I Sbjct: 72 WIDIDFKGLIPGLVSNRFDIAASAIYMTDERRKVVNFSDPYYRGGLAVLVRRDDNSIKVP 131 Query: 129 ADLD-GKKVSVQVGTKSVSYLTEKFPKVQRVEVEKNQEMFNLVDIGRADAAVTGKPAAFQ 187 DL+ GK+VSVQVGTKSV YL + FP V+RVEVEKNQ MF+L+ GR +A VTG+PAA + Sbjct: 132 EDLNKGKRVSVQVGTKSVGYLKDNFPGVERVEVEKNQAMFDLLATGRVNAVVTGRPAAVE 191 Query: 188 YVRTRPGLRVLDEQLTTEEYGMALRKDTPELTKAVNGAITKLKADGTYAAIVKKWFSNS 246 Y RT+P +RVLD+ LTTE YG ALRK ELT +N A+ L+ +GTY A+ KWF S Sbjct: 192 YARTQPLVRVLDKGLTTELYGFALRKSDTELTAQLNKALQTLRMNGTYTALTDKWFGKS 250 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: 242 Number of extensions: 8 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: 251 Length adjustment: 24 Effective length of query: 225 Effective length of database: 227 Effective search space: 51075 Effective search space used: 51075 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: 46 (22.3 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