Align Putative TRAP dicarboxylate transporter, DctM subunit (characterized, see rationale)
to candidate BPHYT_RS24185 BPHYT_RS24185 C4-dicarboxylate ABC transporter permease
Query= uniprot:Q88NP0 (426 letters) >FitnessBrowser__BFirm:BPHYT_RS24185 Length = 450 Score = 306 bits (785), Expect = 6e-88 Identities = 170/445 (38%), Positives = 258/445 (57%), Gaps = 21/445 (4%) Query: 1 MEAFILLGSFIVLILIGMPVAYALGLSALIGAWWIDIPLQAMMIQVASGVNKFSLLAIPF 60 ME IL SF+V +L+G+PV++ LGL+ ++ + +P M + SG+N FS LA+PF Sbjct: 1 MELAILSVSFLVFLLLGVPVSFGLGLACVLTYLYEGLPAATAMQSMISGINGFSFLAVPF 60 Query: 61 FVLAGAIMAEGGMSRRLVAFAGVLVGFVRGGLSLVNIMASTFFGAISGSSVADTASVGSV 120 F+L+G +M GG++ R++ FA VG RGGL + N++A T FG +SGS ADT+++G V Sbjct: 61 FILSGELMLHGGIADRILRFAQATVGHFRGGLGMANVVACTLFGGVSGSPSADTSAMGGV 120 Query: 121 LIPEMERKGYPREFSTAVTVSGSVQALLTPPSHNSVLYSLAAGGT-----------VSIA 169 +IP M+R+GY ++ VT S+ L P S N ++Y+ AA G VSI Sbjct: 121 VIPLMKREGYSAAYAVNVTTHSSLAGALMPTSTNMIIYAFAAQGITGTLNGHPMSGVSIG 180 Query: 170 SLFMAGIMPGLLLSAVMMGLCLIFAKKRNYPKGEVIPLREALKIAG---------EALWG 220 L +G++P L + ++ A K YP+ E K G AL G Sbjct: 181 DLLFSGLLPVLWVMGFVLIAAYWQAVKYGYPR-RADGSTELQKFPGWYAVARTFLGALPG 239 Query: 221 LMAMVIILGGILSGVFTATESAAVAVVWSFFVTMFIYRDYKWRDLPKLMHRTVRTISIVM 280 LM + IIL + G+ TATE+AA+AV +S +T+ +YR + L + + +T +V+ Sbjct: 240 LMVIAIILVCVAKGIATATEAAAIAVFYSLVLTIVVYRSMTMKKLFHALSKAAKTTGVVL 299 Query: 281 ILIGFAASFGYVMTLMQIPSKITTAFLTLSDNRYVILMCINFMLMLLGTVMDMAPLILIL 340 +LIG + Y M ++IP I + +++L+ IN + + LGT +DMA ILI Sbjct: 300 LLIGVSNMLRYQMAYLEIPDAIEHMLDGATSLPWLMLLYINLIQIFLGTFVDMAAHILIT 359 Query: 341 TPILLPVITGIGVDPVHFGMIMLVNLGIGLITPPVGAVLFVGSAIGKVSIESTVKALMPF 400 TP+ LP+ GV PV FG+++L+N +GL+ PP+G+V F+G AIG VSI T K P+ Sbjct: 360 TPLFLPMAMHAGVGPVQFGIMILLNCALGLVHPPIGSVQFIGCAIGNVSIGETTKVAWPY 419 Query: 401 YLALFLVLMAVTYIPAISLWLPSVV 425 YLA+F + VTY+P S WLPS++ Sbjct: 420 YLAIFSAINIVTYVPMFSTWLPSLI 444 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: 545 Number of extensions: 33 Number of successful extensions: 4 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: 450 Length adjustment: 32 Effective length of query: 394 Effective length of database: 418 Effective search space: 164692 Effective search space used: 164692 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