Align TRAP transporter, subunit DctM (characterized, see rationale)
to candidate GFF1297 PGA1_c13130 TRAP transporter, subunit DctM
Query= uniprot:I7DRS6 (467 letters) >FitnessBrowser__Phaeo:GFF1297 Length = 491 Score = 243 bits (621), Expect = 8e-69 Identities = 154/518 (29%), Positives = 249/518 (48%), Gaps = 99/518 (19%) Query: 3 VVLLFSMVIGLLLIGVPIAVAL-GLSSTLFLLIYSDSSLASVAGTLFEAFEGHFTLLAIP 61 ++ + + LLLIG+P+ L L L + L + L+ + F L+AIP Sbjct: 2 LIWFLPLFLFLLLIGLPVFFCLLAAPGALLWLNGQERDLTLLYRNLYNGMDS-FPLMAIP 60 Query: 62 FFILASSFMTTGGVARRIIRFSIACVGHLPGGLAIAGVFACMLFAALSGSSPATVVAIGS 121 FF+LA M GG+ R++ FS A +GHL GGLA + + +LFA LSGS+ A A+GS Sbjct: 61 FFMLAGELMNRGGITVRLVEFSQALMGHLRGGLAQVNILSSILFAGLSGSAVADTSALGS 120 Query: 122 IVIAGMRQVGYSKEFAAGVICNAGTLGILIPPSIVMVVYAAAVEVSVGRMFLAGVIPGLM 181 ++I M + GYS++FAA V + +G +IPPS +M++YA + SV +FLAG++PG++ Sbjct: 121 MLIPAMEREGYSRKFAAAVTAASSVIGPIIPPSGIMIIYAYVMGESVAALFLAGIVPGVL 180 Query: 182 AGLMLMVTIYVMAKVKNLPKG--------------EWLGWGEV--------------AAS 213 G+ LM+ + MA LP W +G V A Sbjct: 181 VGVGLMIMVRAMADRYELPAARRVVFDSVEIGVMERWFSFGLVRLNLGLLLAQFVPLAEG 240 Query: 214 AANASVGLLLIGIIL-----------------------------------GGIYGGIFTP 238 A L G +L GGI G+FTP Sbjct: 241 AGAQMKWLAFFGAVLFAHGLMLGLRRVVSPAFRTICKRAVVPLQTPVLILGGILAGVFTP 300 Query: 239 TEAAAVASVYAFFVATFVYRDMGPLKSAPKPKDMGQFLTMLPKMLGQTVVYFIPSFFHAD 298 TEAAAVA YA ++ V +G ++ A P+ Sbjct: 301 TEAAAVAVAYALLISFLV---LGSMRLADLPQ---------------------------- 329 Query: 299 TRHALFEAGKLTVTLLFVIANALILKHVLTDEQVPQQIATAMLSAGFGPVMFLIVVNVIL 358 AG + +L ++ A+ K V++ P+Q+A +L+ P++ L ++N++L Sbjct: 330 ---VFSRAGITSAVVLLLVGAAMSFKTVVSLSHAPEQLADFILTLSENPLILLFLINLLL 386 Query: 359 LIGGQFMEPSGLLVIVAPLVFPIAIELGIDPIHLGIIMVVNMEIGMITPPVGLNLFVTSG 418 + G F++ ++I+ P++ P+ +LG++ +H IIM VN+ +G+ TPP+GL LFV + Sbjct: 387 FVVGMFLDAGPAIIILGPILGPVFTDLGVESVHFAIIMCVNLTVGLATPPMGLVLFVAAA 446 Query: 419 VAGMPMMAVVRAALPFLAVLFVFLIMITYIPWISTVLP 456 V+ + + +A LPFLA+ + +IT++P IS +P Sbjct: 447 VSQERVTTIAKAILPFLAIEIAVIFLITFVPAISLTIP 484 Score = 25.8 bits (55), Expect = 0.003 Identities = 40/201 (19%), Positives = 81/201 (40%), Gaps = 11/201 (5%) Query: 9 MVIGLLLIGV-----PIAVALGLSSTLFLLIYSDSSLASVAGTLFEAFEGHFTLLAIPFF 63 +++G +L GV AVA+ + + L+ LA + A G + + + Sbjct: 288 LILGGILAGVFTPTEAAAVAVAYALLISFLVLGSMRLADLPQVFSRA--GITSAVVLLLV 345 Query: 64 ILASSFMTTGGVARRIIRFSIACVGHLPGGLAIAGVFACMLFAA--LSGSSPATVVAIGS 121 A SF T ++ + + + L + + +LF + PA ++ +G Sbjct: 346 GAAMSFKTVVSLSHAPEQLADFILTLSENPLILLFLINLLLFVVGMFLDAGPAIII-LGP 404 Query: 122 IVIAGMRQVGYSKEFAAGVICNAGTLGILIPPSIVMVVYAAAVEVSVGRMFLAGVIPGLM 181 I+ +G A ++C T+G+ PP +++ AAAV ++P L Sbjct: 405 ILGPVFTDLGVESVHFAIIMCVNLTVGLATPPMGLVLFVAAAVSQERVTTIAKAILPFLA 464 Query: 182 AGLMLMVTI-YVMAKVKNLPK 201 + ++ I +V A +P+ Sbjct: 465 IEIAVIFLITFVPAISLTIPR 485 Lambda K H 0.329 0.144 0.421 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: 692 Number of extensions: 37 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 4 Number of HSP's successfully gapped: 3 Length of query: 467 Length of database: 491 Length adjustment: 34 Effective length of query: 433 Effective length of database: 457 Effective search space: 197881 Effective search space used: 197881 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 (21.8 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