Align GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP (characterized)
to candidate PfGW456L13_2756 Gamma-aminobutyrate permease
Query= SwissProt::P46349 (469 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2756 Length = 454 Score = 428 bits (1100), Expect = e-124 Identities = 218/443 (49%), Positives = 295/443 (66%), Gaps = 4/443 (0%) Query: 8 LKKELKTRHMTMISIAGVIGAGLFVGSGSVIHSTGPGAVVSYALAGLLVIFIMRMLGEMS 67 L + K RH+TM+SIAG+IGAGLFVGSG I + GP +++Y +GLLV+ +MRMLGEM+ Sbjct: 1 LAQGFKPRHVTMLSIAGIIGAGLFVGSGHAIAAAGPAVLLAYLFSGLLVVLVMRMLGEMA 60 Query: 68 AVNPTSGSFSQYAHDAIGPWAGFTIGWLYWFFWVIVIAIEAIAGAGIIQYWFHDIPLWLT 127 NP +GSFS YA AIG WAGFTIGWLYW+FWV+VI IEA+A ++ WF I WL Sbjct: 61 VANPDTGSFSTYADQAIGRWAGFTIGWLYWWFWVLVIPIEALAAGHVLNQWFPQIDAWLF 120 Query: 128 SLILTIVLTLTNVYSVKSFGEFEYWFSLIKVVTIIAFLIVGFAFIFGFAPGSEPVGFSNL 187 +L+ I L +TN++SV +GEFE+WF++ KVV II F+ VGFA + G+ P E G S L Sbjct: 121 ALVSIIALVITNLFSVSKYGEFEFWFAMAKVVAIIGFIGVGFAVLMGWVPDREVSGLSGL 180 Query: 188 TGK-GGFFPEGISSVLLGIVVVIFSFMGTEIVAIAAGETSNPIESVTKATRSVVWRIIVF 246 + GGF P G+S+V+ + ++FSF+GTE V IAA E+ NP +++ KATRSV+WRI VF Sbjct: 181 MAEHGGFAPNGLSAVVGAFITIMFSFIGTEAVTIAAAESDNPSQNIAKATRSVIWRIGVF 240 Query: 247 YVGSIAIVVALLPWNSANILE-SPFVAVLEHIGVPAAAQIMNFIVLTAVLSCLNSGLYTT 305 Y+ SI +V++++PWN + + + LE + +P A +++ +VL AV SC+NS +Y Sbjct: 241 YLLSIFVVISVVPWNDPLLAQVGSYQRALEIMNIPHAKFMVDVVVLIAVASCMNSSIYIA 300 Query: 306 SRMLYSLAERNEAPRRFMKLSKKGVPVQAIVAGTFFSYIAVVMNYFSPDTVFLFLVNSSG 365 SRMLYSL R +AP+ S +GVP A++A T V +YF P +F FL+ SSG Sbjct: 301 SRMLYSLGRRGDAPKSLKATSSEGVPRAAVIASTVLGAAITVWSYFMPAGLFNFLLASSG 360 Query: 366 AIALLVYLVIAVSQLKMRKKLEKTNPEALKIKMWLFPFLTYLTIIAICGILVSMAFIDSM 425 AIALLVYL IAVSQL+MR+ L + N E L +MWLFP+LT+L I IC L M Sbjct: 361 AIALLVYLAIAVSQLRMRRMLRRQNIE-LTFRMWLFPWLTWLVIAFICAALAVMMITPEH 419 Query: 426 RDELLLT-GVITGIVLISYLVFR 447 R E+ T G+ I I + R Sbjct: 420 RTEVSTTIGLALAISFIGLVTSR 442 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: 645 Number of extensions: 28 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: 454 Length adjustment: 33 Effective length of query: 436 Effective length of database: 421 Effective search space: 183556 Effective search space used: 183556 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