Align HutW aka HISW, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate GFF1016 HP15_995 binding-protein-dependent transport systems inner membrane component
Query= TCDB::Q9KKE2 (285 letters) >FitnessBrowser__Marino:GFF1016 Length = 247 Score = 97.4 bits (241), Expect = 3e-25 Identities = 59/182 (32%), Positives = 97/182 (53%), Gaps = 2/182 (1%) Query: 91 LTMQTLALMLMATIVSVVIGVPMGILVAK--SRVVRNITLPVLDVMQTMPSFVYLIPALM 148 L L L++++ +V V V GI + R + + + QT P L A+ Sbjct: 48 LLQNHLMLVVISALVGTVAAVAGGIFATRPAGRDFLPLVSQIASIGQTFPPVAVLALAVP 107 Query: 149 LFGLGKVPAILATIIYAVPPLIRLTDLGIRQVDAEVVEAATAFGGSPGQILFGVELPLAT 208 + G G+ P ++A I+Y + P++R T G+ VDA V +AA G SP Q+L VELPLA Sbjct: 108 VLGFGEAPILVALILYGLLPILRNTLAGLEGVDATVRQAALGMGMSPFQVLLQVELPLAG 167 Query: 209 PTIMAGLNQTIMMALSMVVVASMIGARGLGEQVLNGIQTLDVGKGLEAGIGIVILAVVLD 268 I+AG+ ++ + ++ + S IGAR LG+ V+ G+ + L+ I I +LA+ +D Sbjct: 168 RVILAGIRTSVTINIATAAIGSTIGARTLGDPVIAGLVNGNTAYVLQGAILIGMLALTVD 227 Query: 269 RI 270 + Sbjct: 228 SL 229 Lambda K H 0.327 0.142 0.422 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: 191 Number of extensions: 7 Number of successful extensions: 1 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: 285 Length of database: 247 Length adjustment: 25 Effective length of query: 260 Effective length of database: 222 Effective search space: 57720 Effective search space used: 57720 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (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