Align arginine permease (characterized)
to candidate RR42_RS33780 RR42_RS33780 GABA permease
Query= CharProtDB::CH_091699 (590 letters) >FitnessBrowser__Cup4G11:RR42_RS33780 Length = 474 Score = 253 bits (646), Expect = 1e-71 Identities = 158/442 (35%), Positives = 227/442 (51%), Gaps = 26/442 (5%) Query: 80 QNAEVKRELKQRHIGMIALGGTIGTGLFIGLSTPLTNAGPVGALISYLFMGSLAYSVTQS 139 Q++ +K LKQRH+ MIALGG IG GLF+G + +AGP A+IS+L G L V + Sbjct: 9 QSSGLKHGLKQRHMTMIALGGVIGAGLFVGSGVVIKSAGPA-AVISFLITGLLVVLVMRM 67 Query: 140 LGEMATFIPVTSSFTVFSQRFLS--PAFGAA----NGYMYWFSWAITFALELSVVGQVIQ 193 LGEMA +P SF +++ S PA G G+MYW+ W I ALE ++Q Sbjct: 68 LGEMACALPTVGSFYEYAREAWSDRPAMGELAGFLTGWMYWYFWVIVVALEAVAGASLVQ 127 Query: 194 FWTYKVPLAAWISIFWVIITIMNLFPVKYYGEFEFWVASIKVLAIIGFLIYCFCMVCGAG 253 FW VP + + V++T+ NL VK +GEFEFW ASIKV AI+ FL V G Sbjct: 128 FWLPGVPAWSISLVLLVMLTLTNLISVKSFGEFEFWFASIKVAAIVVFLFLAGLFVLGMW 187 Query: 254 VTGPVGFRYWRNPGAWGPGIISKDKNEGRFLGWVSSLINAAFTFQGTELVGITAGEAANP 313 + G + P I + ++ + A + G E+V I A E A P Sbjct: 188 PGATASVAHLTVHGGFAPNGI---------MPVLTGAVAATGFYFGAEIVTIAAAETAEP 238 Query: 314 RKSVPRAIKKVVFRILTFYIGSLLFIGLLVPYNDPKLTQSTSYVSTSPFIIAIENSGTKV 373 +K+V RA V+ R+L FY+GS+L + LVP+N + +P++ A+ Sbjct: 239 QKAVARATSSVITRVLVFYVGSVLLVVCLVPWNSAGIA--------TPYVSALNAMRIPA 290 Query: 374 LPHIFNAVILTTIISAANSNIYVGSRILFGLSKNKLAPKFLSRTTKGGVPYIAVFVTAAF 433 I NAV+LT ++SA NS +Y SR+LF L+K APK L+R ++ GVP A+ F Sbjct: 291 AAQIMNAVVLTAVLSALNSGLYASSRMLFALTKRGDAPKALARLSRNGVPVRAILFATLF 350 Query: 434 GALAYMETSTGGDKVFEWLLNITGVAGFFAWLFISISHIRFMQALKYRGISRDELPFKAK 493 G A + + DKVF +L+N G F ++ I+IS +R L+ R L + Sbjct: 351 GYGAVVMSYVSPDKVFAFLVNSYGTVAIFVYILIAISQLRLRARLEREAPHR--LKVRMW 408 Query: 494 LMPGLAYYAATFMTIIIIIQGF 515 P L + A M I++ F Sbjct: 409 AFPYLTWVAIAGMVGIVVAMAF 430 Lambda K H 0.325 0.140 0.438 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: 686 Number of extensions: 44 Number of successful extensions: 5 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: 590 Length of database: 474 Length adjustment: 35 Effective length of query: 555 Effective length of database: 439 Effective search space: 243645 Effective search space used: 243645 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 52 (24.6 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