GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Phyllobacterium brassicacearum STM 196

Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_106711277.1 CU102_RS11775 ATP-binding cassette domain-containing protein

Query= TCDB::O05176
         (512 letters)



>NCBI__GCF_003010955.1:WP_106711277.1
          Length = 509

 Score =  718 bits (1854), Expect = 0.0
 Identities = 371/509 (72%), Positives = 432/509 (84%), Gaps = 2/509 (0%)

Query: 4   TILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGE 63
           TILEMRNITKTFPGVKAL NVNL V++GEIHALVGENGAGKSTLMKVLSGVYP G+YEGE
Sbjct: 3   TILEMRNITKTFPGVKALNNVNLDVRKGEIHALVGENGAGKSTLMKVLSGVYPHGSYEGE 62

Query: 64  IHYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQTFNR 123
           I Y G  ++FR I DSE  GIIIIHQELALVPLLSIAENIFLGNE A  GVI W    NR
Sbjct: 63  IIYNGQEQHFRDIADSERQGIIIIHQELALVPLLSIAENIFLGNEPAKFGVIDWHVAENR 122

Query: 124 TRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALL 183
           TRELL KVGLKE P TLIT++GVGKQQLVEIAKALSK V+LLILDEPTASLNE DS+ALL
Sbjct: 123 TRELLAKVGLKEDPLTLITNLGVGKQQLVEIAKALSKEVELLILDEPTASLNEKDSDALL 182

Query: 184 NLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMVG 243
            LL+EF+  G++SI+I+HKLNEV KVAD+ITVLRDG T++TLD  +++ISED I+ +MVG
Sbjct: 183 ALLLEFKAHGISSILISHKLNEVGKVADRITVLRDGATIETLD--KKDISEDRIVTSMVG 240

Query: 244 RDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAGR 303
           R L DR+P R+  IGE + EVK+W  +H  H DR V++ IN++VRKGEVVGIAGLMGAGR
Sbjct: 241 RQLADRFPQREPDIGEVVFEVKDWVVHHHIHSDRTVINGINLSVRKGEVVGIAGLMGAGR 300

Query: 304 TEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNILH 363
           TEFAMSVFGK+YG +I+G+V + GK VDVST+ KAID G+AYVTEDRK  GL L D+I H
Sbjct: 301 TEFAMSVFGKAYGRKISGEVFLKGKKVDVSTIGKAIDNGIAYVTEDRKTFGLNLIDHIKH 360

Query: 364 NTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSKWL 423
           NTT+ NLAGVS+  ++DD+ E+KVA+++R +  IRSS I+Q+T NLSGGNQQKVVLSKWL
Sbjct: 361 NTTIVNLAGVSQNGVLDDMAELKVANEYRRKTNIRSSSIYQKTGNLSGGNQQKVVLSKWL 420

Query: 424 FSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVMNE 483
           F+NPD+LILDEPTRGIDVGAKYEIYTIINQL ++GK VLMISSEMPELLG CDRIYVMN+
Sbjct: 421 FANPDLLILDEPTRGIDVGAKYEIYTIINQLVSEGKSVLMISSEMPELLGVCDRIYVMNQ 480

Query: 484 GRIVAELPKGEASQESIMRAIMRSGEKNS 512
           GR+V E+P  EASQE IMRAI+R+  K S
Sbjct: 481 GRLVGEMPASEASQEKIMRAIIRAEGKAS 509


Lambda     K      H
   0.316    0.135    0.374 

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: 872
Number of extensions: 31
Number of successful extensions: 6
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: 512
Length of database: 509
Length adjustment: 35
Effective length of query: 477
Effective length of database: 474
Effective search space:   226098
Effective search space used:   226098
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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