Align Inner membrane ABC transporter permease protein YjfF (characterized)
to candidate Pf1N1B4_4287 Inositol transport system permease protein
Query= SwissProt::P37772 (331 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4287 Length = 340 Score = 129 bits (325), Expect = 8e-35 Identities = 97/291 (33%), Positives = 158/291 (54%), Gaps = 24/291 (8%) Query: 31 STRVICNILTDNAFLGIIAVGMTFVILSGGIDLSVGSVIAFTGVFLAKVI--GDFGLS-- 86 S R++ IL + +G++A+G+T VI++ GIDLS GSV+A + + A + DF + Sbjct: 53 SQRLVLMIL-QVSIIGLLAIGVTQVIITTGIDLSSGSVLALSAMIAASLAQTSDFARAVF 111 Query: 87 PLLA-----FPLVLVMGCAF--GAFMGLLIDALKIPAFIITLAGMFFLRGVSYLVSEESI 139 P L P+++ +G GA G +I IP FI TL M RG++ +E Sbjct: 112 PSLTDLPVWIPVIVGLGVGLLAGAINGSIIAITGIPPFIATLGMMVSARGLARYYTE--- 168 Query: 140 PINHPIYDTLSSLAWKIPGGGRLSAMGLLMLAVVVIGIFLAHR-TRFGNQVYAIGGNATS 198 P+ ++ S ++ G G AM +++ VV + +A R T++G YAIGGN + Sbjct: 169 --GQPV--SMLSDSYTAIGHG---AMPVIIFLVVAVIFHIALRYTKYGKYTYAIGGNMQA 221 Query: 199 ANLMGISTRSTTIRIYMLSTGLATLAGIVFSIYTQAGYALAGVGVELDAIASVVIGGTLL 258 A GI+ + + +Y ++ LA LAG+V S G A G+ ELDAIA+ VIGGT L Sbjct: 222 ARTSGINVKRHLVIVYSIAGLLAGLAGVVASARAATGQAGMGMSYELDAIAAAVIGGTSL 281 Query: 259 SGGVGTVLGTLFGVAIQGLIQTYINFDGTLSSWWTKIAIGILLFIFIALQR 309 +GGVG + GT+ G I G++ + F G + ++ I G+++ + + + + Sbjct: 282 AGGVGRITGTVIGALILGVMASGFTFVG-VDAYIQDIIKGLIIVVAVVIDQ 331 Lambda K H 0.329 0.145 0.428 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: 346 Number of extensions: 28 Number of successful extensions: 3 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: 331 Length of database: 340 Length adjustment: 28 Effective length of query: 303 Effective length of database: 312 Effective search space: 94536 Effective search space used: 94536 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 (21.8 bits) S2: 49 (23.5 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