Align GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP (characterized)
to candidate Pf1N1B4_5139 Gamma-aminobutyrate permease
Query= SwissProt::P46349 (469 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5139 Length = 501 Score = 421 bits (1082), Expect = e-122 Identities = 218/457 (47%), Positives = 301/457 (65%), Gaps = 3/457 (0%) Query: 4 SQSGLKKELKTRHMTMISIAGVIGAGLFVGSGSVIHSTGPGAVVSYALAGLLVIFIMRML 63 S L + K RH+TM+SIAG+IGAGLFVGSG I + GP +++Y +GLLV+ +MRML Sbjct: 42 SNGQLAQGFKPRHVTMLSIAGIIGAGLFVGSGHAIAAAGPAVLLAYLFSGLLVVLVMRML 101 Query: 64 GEMSAVNPTSGSFSQYAHDAIGPWAGFTIGWLYWFFWVIVIAIEAIAGAGIIQYWFHDIP 123 GEM+ NP +GSFS YA AIG WAGFTIGWLYW+FWV+VI IEA+A ++ WF I Sbjct: 102 GEMAVANPDTGSFSTYADQAIGRWAGFTIGWLYWWFWVLVIPIEALAAGHVLNQWFPQID 161 Query: 124 LWLTSLILTIVLTLTNVYSVKSFGEFEYWFSLIKVVTIIAFLIVGFAFIFGFAPGSEPVG 183 WL +L I+L +TN++SV +GEFE+WF++ KVV II F+ +GFA + G+ P E G Sbjct: 162 TWLFALTSIILLVVTNLFSVSKYGEFEFWFAMAKVVAIIGFIGLGFAVLMGWIPEREASG 221 Query: 184 FSNLTGK-GGFFPEGISSVLLGIVVVIFSFMGTEIVAIAAGETSNPIESVTKATRSVVWR 242 S L + GGF P G+S+V+ + ++FSF+GTE V IAA E+SNP +++ KATRSV+WR Sbjct: 222 LSRLMEEHGGFAPNGLSAVVGAFITIMFSFIGTEAVTIAAAESSNPAQNIAKATRSVIWR 281 Query: 243 IIVFYVGSIAIVVALLPWNSANILE-SPFVAVLEHIGVPAAAQIMNFIVLTAVLSCLNSG 301 I VFY+ SI +V++++PWN + + LE + +P A +++ +VL AV SC+NS Sbjct: 282 IGVFYLLSIFVVISVVPWNDPLLASVGSYQRALELMNIPHAKLMVDVVVLIAVASCMNSS 341 Query: 302 LYTTSRMLYSLAERNEAPRRFMKLSKKGVPVQAIVAGTFFSYIAVVMNYFSPDTVFLFLV 361 +Y SRML+SL +R +AP+ S GVP A++A T + +YF P +F FL+ Sbjct: 342 IYIASRMLFSLGKRGDAPKPLKVTSSDGVPRAAVIASTVLGAGVTLFSYFMPAGLFQFLL 401 Query: 362 NSSGAIALLVYLVIAVSQLKMRKKLEKTNPEALKIKMWLFPFLTYLTIIAICGILVSMAF 421 SSGAIALLVYLVIAVSQL+MRK L + N L KMWLFP+LT+L I IC L M Sbjct: 402 ASSGAIALLVYLVIAVSQLRMRKILLRQN-VTLTFKMWLFPWLTWLVIAFICAALAVMMV 460 Query: 422 IDSMRDELLLTGVITGIVLISYLVFRKRKVSEKAAAN 458 R E+ T + ++ LV ++ ++A + Sbjct: 461 TPEHRMEVSSTIGLALVISFIGLVTARQHGQPRSAVS 497 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: 663 Number of extensions: 29 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: 501 Length adjustment: 34 Effective length of query: 435 Effective length of database: 467 Effective search space: 203145 Effective search space used: 203145 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: 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