GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtrB in Cupriavidus basilensis 4G11

Align GtrB aka SLL1103, component of Tripartite glutamate:Na+ symporter (characterized)
to candidate RR42_RS15935 RR42_RS15935 C4-dicarboxylate ABC transporter

Query= TCDB::P74224
         (445 letters)



>FitnessBrowser__Cup4G11:RR42_RS15935
          Length = 582

 Score =  365 bits (937), Expect = e-105
 Identities = 202/515 (39%), Positives = 306/515 (59%), Gaps = 80/515 (15%)

Query: 1   MVDYDWLGPMMFVGALVFLGCGYPVAFSLGGVAILFAIIGAALGSFDPIFLSAMPQRIFG 60
           M+  +++ P+MF G +VF+  G+PVAFSL  V + F I+    G F   FL A+P R+FG
Sbjct: 1   MIPLEYMPPLMFGGLVVFMLIGFPVAFSLSAVGLAFGILAIQFGYFPVSFLQAVPSRVFG 60

Query: 61  -IMANGTLLAIPFFIFLGSMLERSGIAEQLLETMGIILGHLRGGLALAVILVGTMLAATT 119
            ++AN  LLAIPFF F+G++LE+ G+AE +L++MG + G +RGGL  +VI+VG +L A T
Sbjct: 61  SVLANELLLAIPFFTFMGAILEKCGLAEDMLDSMGQLFGPVRGGLGYSVIIVGFILGAIT 120

Query: 120 GVVAATVVAMGLISLPIMLRYGYSKELASGVIVASGTLGQIIPPSVVLIVLADQL----- 174
           G VAA V+AM +ISLP+M+RY Y+ + A+GV+ ASGT+ Q++PPS+VL+VLADQL     
Sbjct: 121 GTVAAQVIAMAMISLPVMMRYRYNMKYATGVLAASGTITQLVPPSLVLVVLADQLKTPMG 180

Query: 175 GVSVGDLFIGSLLPGLMMAGSFALYVLIIAWLKPDLAPALPAEVRNIGGQELRRRIVQVM 234
              VG +++G+  P ++    FALY  ++  +KPD  P +P E R + G  L R+ ++ +
Sbjct: 181 SADVGSMYLGAWGPSVIQIALFALYTFVLTRIKPDWLPPVPVEERTLRGWPLWRKCLRGI 240

Query: 235 LPPLVLILLVLGSIFFGIASPTEAGAVGSIGAIALAHFNQ----RLNWKALWEVCDATLR 290
           +P  VLI LVLG+I  GIA+PTE+GA+G++GA+ LA        +L+ + ++ +  A   
Sbjct: 241 IPCAVLIFLVLGTIMLGIATPTESGAMGAVGALVLAVLRDPGFGKLD-RNIYRIGLAATG 299

Query: 291 ITSMVMLILLGSTAFSL--------------------VFRGL------------------ 312
           +  +   +  GS AF +                      RGL                  
Sbjct: 300 VAIIAGTVAFGSHAFRIPLALVYLVITWLLLRAGQLTALRGLIIEAYQSTARITAMVVFI 359

Query: 313 --------------EGDRFMFDLLANLPGGQIGFLAISMITIFILGFFIDFFEIAFIVLP 358
                         +G  ++  +  +LPGG IGFL +  + IF L FF+DFFEIAFIV+P
Sbjct: 360 LIGSTCFSVVFQGVDGGAWVEHMFTSLPGGWIGFLLVVNLFIFFLAFFLDFFEIAFIVVP 419

Query: 359 LFKPVA-----------------EALNLDLIWYGVIVGANLQTSFLTPPFGFALFYLRGV 401
           +  PVA                  A    L+W+GV++  N+QTSF+ PPFGFALFYLRG+
Sbjct: 420 MLAPVAVKVLAPVVADSMGGNPEAAATAALVWFGVMLCVNMQTSFMHPPFGFALFYLRGI 479

Query: 402 APASLTTGQIYRGAVPFIGLQVLVLLLIIIFPALI 436
           AP  + +  IY GA+P++GLQ+++++L++ +P L+
Sbjct: 480 APKEVKSSDIYWGALPWVGLQMIMVVLVMFWPGLV 514


Lambda     K      H
   0.331    0.148    0.443 

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: 838
Number of extensions: 53
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 445
Length of database: 582
Length adjustment: 34
Effective length of query: 411
Effective length of database: 548
Effective search space:   225228
Effective search space used:   225228
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 52 (24.6 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