Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate AZOBR_RS30120 AZOBR_RS30120 C4-dicarboxylate ABC transporter permease
Query= uniprot:Q88NP0 (426 letters) >FitnessBrowser__azobra:AZOBR_RS30120 Length = 427 Score = 372 bits (954), Expect = e-107 Identities = 190/426 (44%), Positives = 274/426 (64%) Query: 1 MEAFILLGSFIVLILIGMPVAYALGLSALIGAWWIDIPLQAMMIQVASGVNKFSLLAIPF 60 ME IL +F +++G+PVA+A+GLSAL + +P+ + Q+ SG+N FS LAIPF Sbjct: 1 MELTILAVTFFGFLVLGIPVAFAIGLSALCTILYEGLPVAVIFQQMMSGMNVFSFLAIPF 60 Query: 61 FVLAGAIMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVGSV 120 FV +G +M GG++ ++VA A +VG +RGGL + N++A T FG ++GS VAD +++G+V Sbjct: 61 FVFSGELMLHGGVADKIVATAKNMVGHIRGGLGMSNVVACTLFGGVAGSPVADVSAMGAV 120 Query: 121 LIPEMERKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGTVSIASLFMAGIMPGL 180 +IP M+R+GY +++ VT ++ L P SHN ++Y+LAAGG SI +L AGI+P L Sbjct: 121 MIPMMKREGYHADYAVNVTTHAALVGALMPTSHNMIIYALAAGGKASIGALIAAGIVPAL 180 Query: 181 LLSAVMMGLCLIFAKKRNYPKGEVIPLREALKIAGEALWGLMAMVIILGGILSGVFTATE 240 LL +G A KR YP G + A GL+ +VIIL GI SGVFTATE Sbjct: 181 LLMVCNLGAAYYVAVKRGYPPGTFPGWSILGRSFAAAAPGLLIVVIILAGITSGVFTATE 240 Query: 241 SAAVAVVWSFFVTMFIYRDYKWRDLPKLMHRTVRTISIVMILIGFAASFGYVMTLMQIPS 300 SA++AV+++ +T F+YR W +TV+T +V++LIG + F Y+M L Q+ Sbjct: 241 SASIAVIYALLLTTFVYRTLTWDHFLAAAAKTVKTTGVVLLLIGVSTMFQYIMGLYQVAE 300 Query: 301 KITTAFLTLSDNRYVILMCINFMLMLLGTVMDMAPLILILTPILLPVITGIGVDPVHFGM 360 +S N VI + IN +L LLGT MDMA ILI TPI LP+ G+DPV FG+ Sbjct: 301 ITGELMAGISTNPLVIFLLINIILFLLGTFMDMASTILICTPIFLPIAMQYGMDPVQFGI 360 Query: 361 IMLVNLGIGLITPPVGAVLFVGSAIGKVSIESTVKALMPFYLALFLVLMAVTYIPAISLW 420 +ML+N +GL TPPVG F+G AIG+VS+ ++++ PFY ALF+ L+ VTY+P SLW Sbjct: 361 VMLINCALGLNTPPVGTTQFIGCAIGEVSVGQVMRSITPFYGALFVTLLLVTYVPTFSLW 420 Query: 421 LPSVVL 426 LP +++ Sbjct: 421 LPHMLM 426 Lambda K H 0.329 0.142 0.418 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: 570 Number of extensions: 24 Number of successful extensions: 2 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: 426 Length of database: 427 Length adjustment: 32 Effective length of query: 394 Effective length of database: 395 Effective search space: 155630 Effective search space used: 155630 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