Align TRAP transporter (characterized, see rationale)
to candidate WP_013010512.1 DACET_RS06125 DUF3394 domain-containing protein
Query= uniprot:A8LI82 (743 letters) >NCBI__GCF_000025725.1:WP_013010512.1 Length = 681 Score = 346 bits (888), Expect = 2e-99 Identities = 206/562 (36%), Positives = 319/562 (56%), Gaps = 34/562 (6%) Query: 185 DLVLAICGVAVATYL-ITIYGTLMRNSTGTPFAPIGISIAAVAGTALIMELTRRVAGMAL 243 D + AI G A A Y+ + G MR G P + A L++E TRR G AL Sbjct: 94 DYIFAILGAAAALYIAVDANGLAMR--AGFPITRD--VVFGFATVILLLEATRRSIGPAL 149 Query: 244 IVIAGIFLAYVFVGQYLPGFLNAPAVTWQRFFSQV-YTDAGILGPTTAVSSTYIILFIIF 302 +IA F AY F+G Y+P F+ V+ ++ +Q+ + GI G VS++ + LF++ Sbjct: 150 TIIALAFSAYAFLGPYMPQFMAFKGVSLNKYLNQISLSTEGIYGIPLGVSASIVYLFVLL 209 Query: 303 AAFLQASKVGDYFVNFAFAAAGQSRGGPAKVAIFASGLMGMINGTSAGNVVATGSLTIPL 362 + L + G +F++ + + G+ +GGPAK AI ASG G+++G+S N+V TG+ TIPL Sbjct: 210 GSMLDKAGAGKFFIDMSLSLLGRFKGGPAKAAIVASGFTGLVSGSSIANIVTTGTFTIPL 269 Query: 363 MKKVGYHKKTAGAVEAAASTGGQIMPPIMGAGAFIMAEITGIPYTEIALAAIIPAILYFV 422 MKKVGY A A E AAST GQ+MPPIMGA AFI+AE +PY E+ AA +PA + + Sbjct: 270 MKKVGYPATKAAATEVAASTDGQLMPPIMGAAAFIIAEYVNVPYIEVVKAAAVPAFVSYF 329 Query: 423 SVYFMVDLEAAKLGMRGMSRDELPKFNKMVRQ-VYLFLPIIILIYAL-FMGYSVIRAGTL 480 +++++ LEA+KLGMRG+++DE PKF +++R + +PI +L+Y L + +S A Sbjct: 330 ALFYVTHLEASKLGMRGLTKDECPKFFEVIRNGAHYLIPIFMLVYELVIVRHSPEMAAYN 389 Query: 481 ATVAAAVVSWFTPFRM-----GPRSIAKAF----------EIAGTMSVQIIAVC-ACAGI 524 A + A++ ++ R G ++ A A I G+ ++ +A+ A AGI Sbjct: 390 AVLILALIIFYQEIRKEFKTGGSKNFAAAMINSIKTIGNGLIGGSRNMVSVALATASAGI 449 Query: 525 IVGVISLTGVGARFSAVLLGIADTSQLLALFFAMCIAILLGMGMPTTAAYAVAASVVAPG 584 IVGV+ + G+G + ++ +A + L L ++LLGMG+PTTA Y V AS+ AP Sbjct: 450 IVGVVGM-GIGGMITQIVETLAQGNIFLLLLITAIASLLLGMGLPTTATYIVMASLTAPI 508 Query: 585 LVQLG------IPLLTAHFFVFYFAVLSAITPPVALASYAAAGISGANPMETSVTSFKIG 638 +V LG IPL+ AH F FYF +L+ TPPV LASYAAA I+ + P+ T + F Sbjct: 509 IVNLGASYGFFIPLMAAHLFCFYFGILADDTPPVGLASYAAAAIADSPPIATGIQGFTYD 568 Query: 639 IAAFIVPFMFFYNSAILMDG--TWFEVLRAGATAVVGVFFLSSGVQGWFMGGRAAWFLRV 696 + I+PFMF +N+ +++ +W + A F ++ +QGWF+ W + Sbjct: 569 LRTAIIPFMFVFNTDLILHNIYSWPLGILIFVMACFAAFAFTAAIQGWFITKNKFWEIPF 628 Query: 697 GLVFAALMLIEGGIMSDLIGVG 718 L+ A +L G + ++G+G Sbjct: 629 -LLATAFILFRPGTLLPILGLG 649 Lambda K H 0.327 0.140 0.419 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: 1317 Number of extensions: 75 Number of successful extensions: 7 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: 743 Length of database: 681 Length adjustment: 39 Effective length of query: 704 Effective length of database: 642 Effective search space: 451968 Effective search space used: 451968 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: 55 (25.8 bits)
This GapMind analysis is from Sep 24 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