Align HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate H281DRAFT_00655 H281DRAFT_00655 putative spermidine/putrescine transport system ATP-binding protein
Query= TCDB::Q9KKE1 (275 letters) >FitnessBrowser__Burk376:H281DRAFT_00655 Length = 359 Score = 171 bits (434), Expect = 2e-47 Identities = 91/237 (38%), Positives = 136/237 (57%), Gaps = 6/237 (2%) Query: 28 LDKADILSRSGCTVGLNDVSLKIGAGKIFVIMGLSGSGKSTLVRHINRLIEPTSGEVLFD 87 L+ I R G V L L + AG+ ++G SGSGK+TL++ I+ L+ P++G + D Sbjct: 5 LEAIGIAKRYGDAVALEPTDLAVQAGEFLTLLGPSGSGKTTLLQMISGLVAPSAGRIEID 64 Query: 88 GDNILDLGAKALRAFRMRRVSMVFQSFALMPHRTVLQNVVYGQRVRGVSKDDAREIGMKW 147 G ++ + R + MVFQS+AL PH +V NV YG R+R S+D+ R Sbjct: 65 GRDVTHVEPGK------RGIGMVFQSYALFPHMSVWDNVAYGLRMRRKSRDEVRGAVDDA 118 Query: 148 IDTVGLSGYDAKFPHQLSGGMKQRVGLARALAADTDVILMDEAFSALDPLIRGDMQDQLL 207 + V ++ Y +FP +LSGG +QR+ LAR A VIL+DE ALD +R MQ ++ Sbjct: 119 LAMVRMTEYAKRFPKELSGGQQQRIALARCFAYRPSVILLDEPLGALDKKLREHMQSEIR 178 Query: 208 QLQRNLAKTIVFITHDLDEALRIGSEIAILRDGQVVQVGTPNDILDNPANDYVARFV 264 +L + L T V++THD DEAL + I ++ ++ QVGTP D+ D PA + A F+ Sbjct: 179 RLHKELGATFVYVTHDQDEALTLSDRICLMNQARIEQVGTPADLYDRPATRFAAGFI 235 Lambda K H 0.323 0.139 0.397 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: 271 Number of extensions: 11 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: 275 Length of database: 359 Length adjustment: 27 Effective length of query: 248 Effective length of database: 332 Effective search space: 82336 Effective search space used: 82336 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 (21.9 bits) S2: 48 (23.1 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