Align ABC transporter for L-Histidine, permease component (characterized)
to candidate PfGW456L13_3149 L-proline glycine betaine ABC transport system permease protein ProW (TC 3.A.1.12.1)
Query= reanno::pseudo5_N2C3_1:AO356_09615 (283 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3149 Length = 282 Score = 198 bits (504), Expect = 1e-55 Identities = 105/284 (36%), Positives = 167/284 (58%), Gaps = 3/284 (1%) Query: 1 MFPESFTFSIADWVNGWVDSLVTNYGDVFRHISDTLLWAIVNLEGLLRMAPWWLMLAIVG 60 M F+ V+ ++ L+ N VF + L ++ + P++++ + Sbjct: 1 MSTPDFSSQFDSVVDSSLEWLMDNGESVFDTTNTFLKGVYEGVQWCIAYPPYYVIAIAIA 60 Query: 61 GIAWHATRKVLATAVIVGL-LFLVGAVGLWDKLMQTLALMLVATLISVLIGIPLGILSAR 119 I W A L A++ GL L +GLW + + TLAL+L +T++++++ IPLG+L+ Sbjct: 61 LIGWRAVG--LRFAILTGLALLFCDVIGLWPETVSTLALVLTSTVLALVVAIPLGVLAGL 118 Query: 120 SNRLRSVLMPLLDIMQTMPSFVYLIPVLMLFGLGKVPAIFATVIYAAPPLIRLTDLGIRQ 179 + V+ P LD++QTMP ++YL+P + L G G A+ AT I A PP +RLT LGIR Sbjct: 119 APSFDRVVDPFLDLIQTMPPYIYLLPAIALLGYGTATALLATFIVAVPPAMRLTSLGIRM 178 Query: 180 VDGEVMEAINAFGANRWQQLFGVQLPLALPSIMAGINQTTMMALSMVVIASMIGARGLGE 239 E +E +A G WQ F ++LP A+PSIMAG+NQ+ MMA MVVIA ++G+ GLGE Sbjct: 179 TPKEFIELGDASGVTGWQMFFKIRLPFAMPSIMAGVNQSLMMAFGMVVIAGIVGSGGLGE 238 Query: 240 DVLVGIQTLNVGRGLEAGLAIVILAVVIDRITQAYGRPRHEVSK 283 + ++TL++ + + A +AIVIL +++DR+ Q+ R R SK Sbjct: 239 SIYGAVRTLDIAKSINAAIAIVILTMILDRLAQSAARSRMGESK 282 Lambda K H 0.328 0.142 0.429 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: 246 Number of extensions: 16 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: 283 Length of database: 282 Length adjustment: 26 Effective length of query: 257 Effective length of database: 256 Effective search space: 65792 Effective search space used: 65792 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