Align Aromatic amino acid transporter AroP (characterized, see rationale)
to candidate Pf6N2E2_4195 transport permease protein of gamma-aminobutyrate
Query= uniprot:A0A2Z5MFR8 (461 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4195 Length = 464 Score = 301 bits (771), Expect = 3e-86 Identities = 164/454 (36%), Positives = 253/454 (55%), Gaps = 3/454 (0%) Query: 1 MDNALQQDGLKRGLKNRHIQLIALGGAIGTGLFLGSASVLQAAGPSMILGYAIGGVIAFM 60 M + L++GLK RH+ ++++ G IG GLF+GS + AAGP+++L YA G + + Sbjct: 1 MSGTQTSNHLEQGLKPRHVTMLSIAGVIGAGLFVGSGHAIAAAGPAVLLAYAAAGALVVL 60 Query: 61 IMRQLGEMVAQEPVAGSFSHFAYKYWGDFPGFLSGWNYWVLYVLVSMAELTAVGTYVHYW 120 +MR LGEM P GSFS +A + G + GF GW YW +VLV E A T +H W Sbjct: 61 VMRMLGEMAVASPDTGSFSTYADRAIGHWAGFTIGWLYWWFWVLVIPLEANAAATILHAW 120 Query: 121 WPGVPTWVSALVCFAGINAINLANVKAYGETEFWFAIIKVVAVIGMILFGGYLLVSGHGG 180 +P V W LV + NL +VK YGE EFWFA++KVVA+IG I G + Sbjct: 121 FPNVAIWAFTLVITLLLTVTNLFSVKNYGEFEFWFALVKVVAIIGFIGLGVMAIFGVLPT 180 Query: 181 PQAS-ISNLWSHGGFFPHGFHGLFTMLAVIMFSFGGLELIGITAAEADEPQKSIPKAVNQ 239 Q S +S+L+ GF P+G + + MFSF G E++ I AAE+ P + I KA N Sbjct: 181 SQVSGVSHLFDTQGFLPNGMGAVLGAILTTMFSFMGTEIVTIAAAESKNPGQQISKATNS 240 Query: 240 VIYRILIFYICSLAVLLSLYPWNE-VAAGGSPFVMIFSQIGSTLTANVLNVVVLTAALSV 298 VI+RI +FY+ S+ ++++L PWN+ + A + + ++G ++++VVL A S Sbjct: 241 VIWRIGLFYLVSIFIVVALVPWNDPLLASVGSYQTVLERMGIPNAKLIVDIVVLVAVTSC 300 Query: 299 YNSGVYANSRMLYGLAEQGNAPRALMKVDRRGVPYMAIGLSALATFTCVIVNYLIPAEAL 358 NS +Y SRM++ L ++G+AP + ++ G PY A+ LS A F V NY+ PA Sbjct: 301 LNSALYTASRMMFSLGKRGDAPAVSQRTNKSGTPYWAVMLSTGAAFLAVFANYVAPAAVF 360 Query: 359 GLLMALVVAALVLNWALISLTHLKSRRAMVAAGETLVFKSFWFPVSNWICLAFMALILVI 418 L+A A +L + +I+++ L+ R+ +A GE + F + FP + + F+ L I Sbjct: 361 DFLLASSGAIALLVYLVIAVSQLRMRKQRMARGEKVAFSMWLFPGLTYAVIVFIVGALTI 420 Query: 419 LAMTPGLSVSVLLVPLW-LVVMWAGYAFKRRRAA 451 + V +L L ++V+ +G +RRR A Sbjct: 421 MLFQEAHRVEILATGLLSVLVVISGVLVQRRRIA 454 Lambda K H 0.327 0.140 0.440 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: 461 Number of extensions: 21 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 461 Length of database: 464 Length adjustment: 33 Effective length of query: 428 Effective length of database: 431 Effective search space: 184468 Effective search space used: 184468 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