Align putrescine transport system permease protein PotH (characterized)
to candidate 5208463 Shew_0975 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= CharProtDB::CH_088338 (317 letters) >FitnessBrowser__PV4:5208463 Length = 301 Score = 387 bits (993), Expect = e-112 Identities = 181/292 (61%), Positives = 236/292 (80%) Query: 22 QLQMKHGRKLVIALPYIWLILLFLLPFLIVFKISLAEMARAIPPYTELMEWADGQLSITL 81 + ++ G+ I +PY WL++ F LPF IV KISL+ A AIPPY L ++AD L I L Sbjct: 6 KFRLPKGQCWTIGVPYFWLLMFFALPFAIVLKISLSTPAVAIPPYEALYQYADESLQIML 65 Query: 82 NLGNFLQLTDDPLYFDAYLQSLQVAAISTFCCLLIGYPLAWAVAHSKPSTRNILLLLVIL 141 NLGN++ + +D LY +AYL SL++A ++T CLLIGYP+A+A+A + + +L+LLV+L Sbjct: 66 NLGNYILIFEDHLYINAYLGSLKMACVTTIGCLLIGYPMAYAIARAPKQHQTVLILLVML 125 Query: 142 PSWTSFLIRVYAWMGILKNNGVLNNFLLWLGVIDQPLTILHTNLAVYIGIVYAYVPFMVL 201 PSWTSFLIRVYAWMGIL NNGV+NN L+WLGVI +P+ +L+TN AVYIGI+Y Y+PFM+L Sbjct: 126 PSWTSFLIRVYAWMGILSNNGVINNLLMWLGVISEPIQMLNTNFAVYIGIIYTYLPFMIL 185 Query: 202 PIYTALIRIDYSLVEAALDLGARPLKTFFTVIVPLTKGGIIAGSMLVFIPAVGEFVIPEL 261 P+Y L ++D SL+EAA DLG+R L TF+ V +PL+KGG+IAGSMLVFIP VGEFVIPEL Sbjct: 186 PLYANLSQLDGSLLEAAADLGSRSLNTFWKVTLPLSKGGVIAGSMLVFIPVVGEFVIPEL 245 Query: 262 LGGPDSIMIGRVLWQEFFNNRDWPVASAVAIIMLLLLIVPIMWFHKHQQKSV 313 LGGPDS+MIG+VLWQEFFNNRDWPVAS++AI+ML LLI+PI FH++Q +S+ Sbjct: 246 LGGPDSLMIGKVLWQEFFNNRDWPVASSLAIVMLALLIIPITLFHRYQSRSM 297 Lambda K H 0.328 0.144 0.457 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: 369 Number of extensions: 17 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: 317 Length of database: 301 Length adjustment: 27 Effective length of query: 290 Effective length of database: 274 Effective search space: 79460 Effective search space used: 79460 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: 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