GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Cup4G11:RR42_RS15935
          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:

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