Align GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP (characterized)
to candidate PP_4106 PP_4106 gamma-aminobutyrate permease
Query= SwissProt::P46349 (469 letters) >FitnessBrowser__Putida:PP_4106 Length = 460 Score = 447 bits (1151), Expect = e-130 Identities = 229/456 (50%), Positives = 312/456 (68%), Gaps = 2/456 (0%) Query: 2 NQSQSGLKKELKTRHMTMISIAGVIGAGLFVGSGSVIHSTGPGAVVSYALAGLLVIFIMR 61 N+ Q L+ L +R ++MISIAG+IGAGLF+GS + I + GP ++SYA+ GLLV+ +MR Sbjct: 6 NKKQRSLQHGLTSRQVSMISIAGIIGAGLFIGSSNAIATAGPAILISYAMTGLLVLLVMR 65 Query: 62 MLGEMSAVNPTSGSFSQYAHDAIGPWAGFTIGWLYWFFWVIVIAIEAIAGAGIIQYWFHD 121 MLGEM+ NP SGSFS YA +AIGPWAGFTIGWLYW+FWV++I +EAIAGA I+ +F Sbjct: 66 MLGEMAIANPNSGSFSTYASEAIGPWAGFTIGWLYWWFWVLIIPVEAIAGADILHAYFPG 125 Query: 122 IPLWLTSLILTIVLTLTNVYSVKSFGEFEYWFSLIKVVTIIAFLIVGFAFIFGFAPGSEP 181 +P WL + ++ +VL+ TN+ SVK+FG FEYWF+L+KVV II F+ V +FGF P +E Sbjct: 126 VPSWLFAFLIMLVLSGTNLVSVKNFGAFEYWFALVKVVAIIGFIGVCTLAVFGFWPLAEV 185 Query: 182 VGFSNLTGKGGFFPEGISSVLLGIVVVIFSFMGTEIVAIAAGETSNPIESVTKATRSVVW 241 G S L GGF P G +VL G+++ IFSF G EIV IAA ET+NP + + +AT VV+ Sbjct: 186 SGVSRLWDSGGFMPNGFGTVLGGVLITIFSFFGAEIVTIAADETANPKDKIRRATNLVVY 245 Query: 242 RIIVFYVGSIAIVVALLPWNSANI-LESPFVAVLEHIGVPAAAQIMNFIVLTAVLSCLNS 300 RI +FY+ SI +VV+L+ WN + F VLE + VP A +++ +VL AV SC+NS Sbjct: 246 RIAIFYLASIFLVVSLVAWNDPGLKAVGSFQRVLEVLNVPGAKLLVDLVVLVAVTSCMNS 305 Query: 301 GLYTTSRMLYSLAERNEAPRRFMKLSKKGVPVQAIVAGTFFSYIAVVMNYFSPDTVFLFL 360 GLYT SRMLYSL R +A ++S GVP A++ T + +NY P VF FL Sbjct: 306 GLYTASRMLYSLGARGQALSVTKRISGSGVPTVAVIFSTLAGFAGCFVNYVFPGKVFGFL 365 Query: 361 VNSSGAIALLVYLVIAVSQLKMRKKLEKTNPEALKIKMWLFPFLTYLTIIAICGILVSMA 420 ++++GAIALLVYLVIAVSQL+MR + E+ L++KMWLFP+LT+L I I +L M Sbjct: 366 LSTTGAIALLVYLVIAVSQLRMRARAEREG-RPLELKMWLFPWLTWLVIGTIVMVLGYML 424 Query: 421 FIDSMRDELLLTGVITGIVLISYLVFRKRKVSEKAA 456 F D+ R E L+T +T +L+ L R+ K+ + A Sbjct: 425 FSDAYRYETLMTAGVTAFILLVSLTQRRAKMVAQTA 460 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: 666 Number of extensions: 34 Number of successful extensions: 3 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: 460 Length adjustment: 33 Effective length of query: 436 Effective length of database: 427 Effective search space: 186172 Effective search space used: 186172 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