Align GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP (characterized)
to candidate RR42_RS33780 RR42_RS33780 GABA permease
Query= SwissProt::P46349 (469 letters) >FitnessBrowser__Cup4G11:RR42_RS33780 Length = 474 Score = 490 bits (1261), Expect = e-143 Identities = 246/464 (53%), Positives = 333/464 (71%), Gaps = 10/464 (2%) Query: 3 QSQSGLKKELKTRHMTMISIAGVIGAGLFVGSGSVIHSTGPGAVVSYALAGLLVIFIMRM 62 Q SGLK LK RHMTMI++ GVIGAGLFVGSG VI S GP AV+S+ + GLLV+ +MRM Sbjct: 8 QQSSGLKHGLKQRHMTMIALGGVIGAGLFVGSGVVIKSAGPAAVISFLITGLLVVLVMRM 67 Query: 63 LGEMSAVNPTSGSFSQYAHDA------IGPWAGFTIGWLYWFFWVIVIAIEAIAGAGIIQ 116 LGEM+ PT GSF +YA +A +G AGF GW+YW+FWVIV+A+EA+AGA ++Q Sbjct: 68 LGEMACALPTVGSFYEYAREAWSDRPAMGELAGFLTGWMYWYFWVIVVALEAVAGASLVQ 127 Query: 117 YWFHDIPLWLTSLILTIVLTLTNVYSVKSFGEFEYWFSLIKVVTIIAFLIVGFAFIFGFA 176 +W +P W SL+L ++LTLTN+ SVKSFGEFE+WF+ IKV I+ FL + F+ G Sbjct: 128 FWLPGVPAWSISLVLLVMLTLTNLISVKSFGEFEFWFASIKVAAIVVFLFLAGLFVLGMW 187 Query: 177 PGSEPVGFSNLTGKGGFFPEGISSVLLGIVVVIFSFMGTEIVAIAAGETSNPIESVTKAT 236 PG+ ++LT GGF P GI VL G V + G EIV IAA ET+ P ++V +AT Sbjct: 188 PGAT-ASVAHLTVHGGFAPNGIMPVLTGAVAATGFYFGAEIVTIAAAETAEPQKAVARAT 246 Query: 237 RSVVWRIIVFYVGSIAIVVALLPWNSANILESPFVAVLEHIGVPAAAQIMNFIVLTAVLS 296 SV+ R++VFYVGS+ +VV L+PWNSA I +P+V+ L + +PAAAQIMN +VLTAVLS Sbjct: 247 SSVITRVLVFYVGSVLLVVCLVPWNSAGIA-TPYVSALNAMRIPAAAQIMNAVVLTAVLS 305 Query: 297 CLNSGLYTTSRMLYSLAERNEAPRRFMKLSKKGVPVQAIVAGTFFSYIAVVMNYFSPDTV 356 LNSGLY +SRML++L +R +AP+ +LS+ GVPV+AI+ T F Y AVVM+Y SPD V Sbjct: 306 ALNSGLYASSRMLFALTKRGDAPKALARLSRNGVPVRAILFATLFGYGAVVMSYVSPDKV 365 Query: 357 FLFLVNSSGAIALLVYLVIAVSQLKMRKKLEKTNPEALKIKMWLFPFLTYLTIIAICGIL 416 F FLVNS G +A+ VY++IA+SQL++R +LE+ P LK++MW FP+LT++ I + GI+ Sbjct: 366 FAFLVNSYGTVAIFVYILIAISQLRLRARLEREAPHRLKVRMWAFPYLTWVAIAGMVGIV 425 Query: 417 VSMAFIDSMRDELLLTGVITGIVLISYLVFRKRKVSEKAAANPV 460 V+MAFI R LLL GI++++Y V ++++ + AAA P+ Sbjct: 426 VAMAFIPDQRTPLLLGVASLGILVVAYAV--RQQLRKHAAAAPL 467 Lambda K H 0.326 0.140 0.417 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: 678 Number of extensions: 23 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: 469 Length of database: 474 Length adjustment: 33 Effective length of query: 436 Effective length of database: 441 Effective search space: 192276 Effective search space used: 192276 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: 51 (24.3 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