Align GABA permease; 4-amino butyrate transport carrier; Gamma-aminobutyrate permease; Proline transporter GabP (characterized)
to candidate Pf6N2E2_4959 S-methylmethionine permease
Query= SwissProt::P46349 (469 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4959 Length = 476 Score = 333 bits (854), Expect = 7e-96 Identities = 172/469 (36%), Positives = 281/469 (59%), Gaps = 19/469 (4%) Query: 4 SQSGLKKELKTRHMTMISIAGVIGAGLFVGSGSVIHSTGP-GAVVSYALAGLLVIFIMRM 62 +++G K+E++TRH+ M+++ GVIG GLF+ SG ++ GP GAV++Y + L+V +M Sbjct: 10 TRAGFKQEMQTRHIVMLALGGVIGTGLFLTSGYTVNQAGPMGAVIAYIIGALMVYMVMMC 69 Query: 63 LGEMSAVNPTSGSFSQYAHDAIGPWAGFTIGWLYWFFWVIVIAIEAIAGAGIIQYWFHDI 122 LGE++ P +GSFS YA +GP G+T+ WLYW W + I E A ++ WF D Sbjct: 70 LGELAVQMPETGSFSTYATRFLGPGTGYTVAWLYWLTWTVAIGSEFTAAGILMSRWFPDT 129 Query: 123 PLWLTSLILTIVLTLTNVYSVKSFGEFEYWFSLIKVVTIIAFLIVGFAFIFGFA--PGSE 180 P+W+ S + V+ L+NV SV+ F E E+W SLIKV+T++ FL++G I G + Sbjct: 130 PVWIWSALFAGVVFLSNVISVRLFAETEFWLSLIKVLTVVVFLLIGGGAILGLLNIDQAH 189 Query: 181 PVGFSNLTGKGGFFPEGISSVLLGIVVVIFSFMGTEIVAIAAGETSNPIESVTKATRSVV 240 +G SN T + G FP G + + ++ V F+F GTE++ IAAGET +P +V +A R+ V Sbjct: 190 SIGLSNFT-REGLFPTGFMPIAMTLLAVSFAFSGTELIGIAAGETKDPQRNVPRAIRTTV 248 Query: 241 WRIIVFYVGSIAIVVALLPWNSANILESPFVAVLEHIGVPAAAQIMNFIVLTAVLSCLNS 300 R+ VF+VG+I ++ LLP A ++ESPFV V +IG+P +A IMNF++++A+LS NS Sbjct: 249 LRLAVFFVGTIFVLATLLPREQAGLVESPFVTVFTYIGIPYSADIMNFVIISALLSAANS 308 Query: 301 GLYTTSRMLYSLAERNEAPRRFMKLSKKGVPVQAIVAGTFFSYIAVVMNYFSPDTVFLFL 360 GLY SRML++L+++ P++F L++ G P+ AI+ +++ + F+ DT++L L Sbjct: 309 GLYAASRMLWTLSDQGHLPKQFSALTRMGTPLNAIIVSMAGGAASLLSSVFAADTIYLAL 368 Query: 361 VNSSGAIALLVYLVIAVSQLKMRKKLEKTNPEALKIKMWL--FPFLTYLTIIAICGILVS 418 V+ SG ++V++ IA SQ+ R+ + K+K + +P++ ++ + Sbjct: 369 VSISGLAVVVVWMSIAASQIAFRRHYVANGGDIRKLKFRVRGYPWVPLGALVCCSLACIG 428 Query: 419 MAFIDSMRDELLLTGVITGIVLISYLVF--------RKRKVSEKAAANP 459 +AF R L G+ I++ F R+R++S A P Sbjct: 429 IAFDPEQRVALYF-----GLPFIAWCYFVYYITRKSRERRLSVAFVAQP 472 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: 587 Number of extensions: 24 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: 476 Length adjustment: 33 Effective length of query: 436 Effective length of database: 443 Effective search space: 193148 Effective search space used: 193148 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