Align tryptophan permease (characterized)
to candidate RR42_RS11100 RR42_RS11100 gamma-aminobutyrate permease
Query= CharProtDB::CH_091156 (592 letters) >FitnessBrowser__Cup4G11:RR42_RS11100 Length = 509 Score = 261 bits (666), Expect = 6e-74 Identities = 147/440 (33%), Positives = 237/440 (53%), Gaps = 17/440 (3%) Query: 77 NLKRTLKPRHLIMIAIGGSIGTGLFVGSGKAIAEGGPLGVVIGWAIAGSQIIGTIHGLGE 136 +L+R LK RHL MIAIGG++GTGLFV SG +I++ GP G ++ + + G + + LGE Sbjct: 17 DLQRKLKARHLTMIAIGGAVGTGLFVASGASISQAGPGGALLMYCLIGLMVYCLMTSLGE 76 Query: 137 ITVRFPVVGAFANYGTRFLDPSISFVVSTIYVLQWFFVLPLEIIAAAMTVQYWNSSIDPV 196 + V PV G+F Y +++ F + Y + +E+ AA + +QYW + V Sbjct: 77 LAVHMPVAGSFVTYSALYVEEGFGFALGWSYWFSLAVTIAVELAAAQLVMQYWFPHVSGV 136 Query: 197 IWVAIFYAVIVSINLFGVRGFGEAEFAFSTIKAITVCGFIILCVVLICG---GGPDHEFI 253 +W A F ++ +N F VRGFGEAE+ F+ IK T+ F+ +++I G GGP Sbjct: 137 VWSAGFLLLMFGLNAFSVRGFGEAEYWFALIKVATILIFLAAGLMMIFGIMQGGPQ---- 192 Query: 254 GAKYWHD----PGCLANGFPGVLSVLVVASYSLGGIEMTCLASGE-TDP-KGLPSAIKQV 307 WH+ G P + V ++A +S G E +A+GE DP + +P AI+Q Sbjct: 193 --SGWHNFTLGDAPFVGGIPAMFGVAMIAGFSFQGTETVGVAAGEAADPARTIPRAIRQT 250 Query: 308 FWRILFFFLISLTLVGFLVPYTNQNLLGGSSVD--NSPFVIAIKLHHIKALPSIVNAVIL 365 FWRIL F+++++ ++G L+PYT+ +LL D SPF + + + ++NAV+L Sbjct: 251 FWRILLFYVLAILIIGVLIPYTDPSLLRNDVTDIGVSPFALVFRHAGLAFAAGLMNAVVL 310 Query: 366 ISVLSVGNSCIFASSRTLCSMAHQGLIPWWFGYIDRAGRPLVGIMANSLFGLLAFLVKSG 425 ++LS G S ++AS+R L +A G P + G P V + A + G L FL Sbjct: 311 TALLSAGTSSMYASTRILYGLAVSGRAPRALARLSANGVPYVALFATTAVGALCFLSSLF 370 Query: 426 SMSEVFNWLMAIAGLATCIVWLSINLSHIRFRLAMKAQGKSLDELEFVSAVGIWGSAYSA 485 V+ WL+ +G+ I WL I +SH RFR + QG +L + S + +G ++ Sbjct: 371 GDKAVYLWLLNTSGMTGFIAWLGIAISHYRFRRGLVHQGYKPSDLAYRSPLYPFGPLFAI 430 Query: 486 LINCLILIAQFYCSLWPIGG 505 ++ +I++ Q Y + + G Sbjct: 431 VLCVVIVLGQNYQAFSDVRG 450 Lambda K H 0.326 0.141 0.447 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: 768 Number of extensions: 36 Number of successful extensions: 4 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: 592 Length of database: 509 Length adjustment: 36 Effective length of query: 556 Effective length of database: 473 Effective search space: 262988 Effective search space used: 262988 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 (21.6 bits) S2: 53 (25.0 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