GapMind for catabolism of small carbon sources

 

Aligments for a candidate for dctM in Cupriavidus basilensis 4G11

Align TRAP C4-dicarboxylate transport system permease, DctM-2 subunit, component of The 2-ketomonocarboxylate transporter (presented in order of affinity - 2-oxovalerate [highest affinity, KD=0.1 μM], 2-oxoisovalerate, 2-oxobutyrate, 2-oxoisocaproate, 2-oxo-3-methylvalerate, pyruvate [lowest affinity, KD=3 μM]) (characterized)
to candidate RR42_RS15935 RR42_RS15935 C4-dicarboxylate ABC transporter

Query= TCDB::D5ATK1
         (611 letters)



>lcl|FitnessBrowser__Cup4G11:RR42_RS15935 RR42_RS15935
           C4-dicarboxylate ABC transporter
          Length = 582

 Score =  418 bits (1074), Expect = e-121
 Identities = 265/625 (42%), Positives = 365/625 (58%), Gaps = 103/625 (16%)

Query: 10  MAPIMFVSLIVFLLLGYPVAFSLAANGLVFFIIGVELA--PLSGGSINLDWPLLNAMPER 67
           M P+MF  L+VF+L+G+PVAFSL+A GL F I+ ++    P+S          L A+P R
Sbjct: 7   MPPLMFGGLVVFMLIGFPVAFSLSAVGLAFGILAIQFGYFPVS---------FLQAVPSR 57

Query: 68  FWG-VLSNETLLAIPFFTFMGILLEKSGMAEDLLDTIGQLFGPIRGGLAYAVILVGALLA 126
            +G VL+NE LLAIPFFTFMG +LEK G+AED+LD++GQLFGP+RGGL Y+VI+VG +L 
Sbjct: 58  VFGSVLANELLLAIPFFTFMGAILEKCGLAEDMLDSMGQLFGPVRGGLGYSVIIVGFILG 117

Query: 127 ATTGVVAASVIAMGLISLPIMLRYGYDRRIASGVIAASGTLAQIIPPSLVLIVLADQL-- 184
           A TG VAA VIAM +ISLP+M+RY Y+ + A+GV+AASGT+ Q++PPSLVL+VLADQL  
Sbjct: 118 AITGTVAAQVIAMAMISLPVMMRYRYNMKYATGVLAASGTITQLVPPSLVLVVLADQLKT 177

Query: 185 ---GRSVGDMYKGALIPGLVLTGLYMLYVLVMSILRPNSMPALPKEARTLGQGVLSFFVA 241
                 VG MY GA  P ++   L+ LY  V++ ++P+ +P +P E RTL    L     
Sbjct: 178 PMGSADVGSMYLGAWGPSVIQIALFALYTFVLTRIKPDWLPPVPVEERTLRGWPLWRKCL 237

Query: 242 MGI---GIAIFVAAQHWLAGTGAAKNAGILAASIAVIFVYVMALIDKATG-LDRMSH--- 294
            GI    + IF+     + G      +G + A  A++   +  L D   G LDR  +   
Sbjct: 238 RGIIPCAVLIFLVLGTIMLGIATPTESGAMGAVGALV---LAVLRDPGFGKLDRNIYRIG 294

Query: 295 LAQQVIIVLIP-----------PLALIFLVLGTIFLGIATPTEGGAMGAVGALILSAVKK 343
           LA   + ++             PLAL++LV+  + L        G + A+  LI+     
Sbjct: 295 LAATGVAIIAGTVAFGSHAFRIPLALVYLVITWLLL------RAGQLTALRGLII----- 343

Query: 344 RLSLEVVREALAATTRLSAFVMFILLGARVFSLTFYGVNGHIWVEHLLVSLPGGETGFLI 403
                   EA  +T R++A V+FIL+G+  FS+ F GV+G  WVEH+  SLPGG  GFL+
Sbjct: 344 --------EAYQSTARITAMVVFILIGSTCFSVVFQGVDGGAWVEHMFTSLPGGWIGFLL 395

Query: 404 FVSLLVFFLAFFLDFFELAFIIVPLLVA-----------------PAEALGIDLIWFGVI 446
            V+L +FFLAFFLDFFE+AFI+VP+L                   P  A    L+WFGV+
Sbjct: 396 VVNLFIFFLAFFLDFFEIAFIVVPMLAPVAVKVLAPVVADSMGGNPEAAATAALVWFGVM 455

Query: 447 LGVNMQTSFMHPPFGFALFFLRSVAPKVPFLDKVTGKLTEPVKTSQIYWGAVPFVCIQIV 506
           L VNMQTSFMHPPFGFALF+LR +APK              VK+S IYWGA+P+V +Q++
Sbjct: 456 LCVNMQTSFMHPPFGFALFYLRGIAPK-------------EVKSSDIYWGALPWVGLQMI 502

Query: 507 MIAVVIAFPQLVMHY--KGKPVDVSHVTVTVPGGIGGGLGGGLGMPGGLGLPPIGAQPGA 564
           M+ +V+ +P LV  +  KG     +   VT+P G G   GG   +P    +P   ++PG 
Sbjct: 503 MVVLVMFWPGLVTMFLDKGSLHHSNAAEVTIPLG-GESPGGAASVPA--PVPGGRSEPGT 559

Query: 565 VPAPGGLGGLPPGLGAPA-GQPVTP 588
           +  P           APA  +P TP
Sbjct: 560 LELP----------AAPADSEPATP 574


Lambda     K      H
   0.327    0.146    0.437 

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: 955
Number of extensions: 68
Number of successful extensions: 7
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: 611
Length of database: 582
Length adjustment: 37
Effective length of query: 574
Effective length of database: 545
Effective search space:   312830
Effective search space used:   312830
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: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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