Align HutW aka HISW, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized)
to candidate Pf1N1B4_1584 Histidine ABC transporter, permease protein (TC 3.A.1)
Query= TCDB::Q9KKE2 (285 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1584 Length = 283 Score = 353 bits (905), Expect = e-102 Identities = 177/280 (63%), Positives = 223/280 (79%) Query: 1 MFPDSLNLSIRAPVNDFIQALVTNYGWVFKAISGVILKAVLFIEWILRGLPWWLVILAFM 60 MFP+S SI VN ++ LVTNYG VF++IS +L A++ +E +LR PWWL++ Sbjct: 1 MFPESFTFSIADWVNSWVDTLVTNYGDVFRSISDTLLWAIVNLEGLLRAAPWWLMLAIVA 60 Query: 61 ALACRSSRRWSLTLAVCALLETVGVLGIWDLTMQTLALMLMATIVSVVIGVPMGILVAKS 120 +A ++R+ T + LL VG +G+WD MQTLALM++AT++SV+IG+P+GIL A+S Sbjct: 61 GVAWHATRKVVTTSVIVGLLFLVGAVGLWDKLMQTLALMMVATVISVLIGIPLGILSARS 120 Query: 121 RVVRNITLPVLDVMQTMPSFVYLIPALMLFGLGKVPAILATIIYAVPPLIRLTDLGIRQV 180 +R++ +P+LD+MQTMPSFVYLIP LMLFGLGKVPAI AT+IYA PPLIRLTDLGIRQV Sbjct: 121 NRLRSVLMPLLDIMQTMPSFVYLIPVLMLFGLGKVPAIFATVIYAAPPLIRLTDLGIRQV 180 Query: 181 DAEVVEAATAFGGSPGQILFGVELPLATPTIMAGLNQTIMMALSMVVVASMIGARGLGEQ 240 D EV+EA AFG + Q LFGV+LPLA P+IMAG+NQT MMALSMVV+ASMIGARGLGE Sbjct: 181 DGEVMEAINAFGANRWQQLFGVQLPLALPSIMAGINQTTMMALSMVVIASMIGARGLGED 240 Query: 241 VLNGIQTLDVGKGLEAGIGIVILAVVLDRITQGFGKPRTE 280 VL GIQTL+VG+GLEAG+ IVILAVV+DRITQ +G+PR E Sbjct: 241 VLVGIQTLNVGRGLEAGLAIVILAVVIDRITQAYGRPRHE 280 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: 311 Number of extensions: 13 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: 283 Length adjustment: 26 Effective length of query: 259 Effective length of database: 257 Effective search space: 66563 Effective search space used: 66563 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