Align Valine amino-acid permease; Branched-chain amino-acid permease 3 (characterized)
to candidate Pf1N1B4_5139 Gamma-aminobutyrate permease
Query= SwissProt::P41815 (604 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5139 Length = 501 Score = 169 bits (428), Expect = 3e-46 Identities = 117/418 (27%), Positives = 198/418 (47%), Gaps = 14/418 (3%) Query: 69 EDNDLEDGTKSMKSNNHLKKSMKSRHVVMMSLGTGIGTGLLVANAKGLSLAGPGSLVIGY 128 E + S SN L + K RHV M+S+ IG GL V + ++ AGP ++++ Y Sbjct: 29 EQKKTMNNLNSRDSNGQLAQGFKPRHVTMLSIAGIIGAGLFVGSGHAIAAAGP-AVLLAY 87 Query: 129 VMVSFVTYFMVQAAGEMGVTYPTLPGNFNAYNSIFISKSFGFATTWLFCIQWLTVLPLEL 188 + + +++ GEM V P G+F+ Y I + GF WL+ W+ V+P+E Sbjct: 88 LFSGLLVVLVMRMLGEMAVANPDT-GSFSTYADQAIGRWAGFTIGWLYWWFWVLVIPIEA 146 Query: 189 ITSSMTVKYWNDTINADVFIVIFYVFLLFIHFFGVKAYGETEFIFNSCKILMVAGFIILS 248 + + + W I+ +F + + L+ + F V YGE EF F K++ + GFI L Sbjct: 147 LAAGHVLNQWFPQIDTWLFALTSIILLVVTNLFSVSKYGEFEFWFAMAKVVAIIGFIGLG 206 Query: 249 VVINCGGAGVDGYIG-GKYWRDPGSFAEGSGATRFKGICYILVSAYFSFGGIELFVLSIN 307 + G G + + G FA + ++ FSF G E ++ Sbjct: 207 FAVLMGWIPEREASGLSRLMEEHGGFAPNG----LSAVVGAFITIMFSFIGTEAVTIAAA 262 Query: 308 EQSNPRKSTPVAAKRSVYRILIIYLLTMILIGFNVPHNNDQLMGSGGSATHASPYVLAAS 367 E SNP ++ A + ++RI + YLL++ ++ VP ND L+ S GS Y A Sbjct: 263 ESSNPAQNIAKATRSVIWRIGVFYLLSIFVVISVVPW-NDPLLASVGS------YQRALE 315 Query: 368 IHKVRVIPHIINAVILISVISVANSALYAAPRLMCSLAQQGYAPKFLNYIDREGRPLRAL 427 + + +++ V+LI+V S NS++Y A R++ SL ++G APK L +G P A+ Sbjct: 316 LMNIPHAKLMVDVVVLIAVASCMNSSIYIASRMLFSLGKRGDAPKPLKVTSSDGVPRAAV 375 Query: 428 VVCSLVGVVGFVACSPQEEQAFTWLAAIAGLSELFTWSGIMLSHIRFRKAMKVQGRSL 485 + +++G + F +L A +G L + I +S +R RK + Q +L Sbjct: 376 IASTVLGAGVTLFSYFMPAGLFQFLLASSGAIALLVYLVIAVSQLRMRKILLRQNVTL 433 Lambda K H 0.324 0.138 0.420 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: 600 Number of extensions: 33 Number of successful extensions: 5 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: 604 Length of database: 501 Length adjustment: 36 Effective length of query: 568 Effective length of database: 465 Effective search space: 264120 Effective search space used: 264120 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 53 (25.0 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