Alignments for a candidate for gguA in Phyllobacterium brassicacearum STM 196

GapMind for catabolism of small carbon sources

Alignments for a candidate for gguA 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_106713128.1 CU102_RS21415 sugar ABC transporter ATP-binding protein

Query= TCDB::O05176
         (512 letters)



>NCBI__GCF_003010955.1:WP_106713128.1
          Length = 516

 Score =  351 bits (900), Expect = e-101
 Identities = 207/500 (41%), Positives = 308/500 (61%), Gaps = 26/500 (5%)

Query: 5   ILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSG-VYPAGTYEGE 63
           +LE R I K F  V+ L +++L V  GE+HA++GENGAGKSTLMK++SG + P     G 
Sbjct: 14  VLEARGIAKAFGPVEVLTDISLTVMPGEVHAIIGENGAGKSTLMKLMSGHLQPT---RGT 70

Query: 64  IHYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQTFNR 123
           +  +G   +F    D+E  G++++HQE+ L P L++A+NIF+G E+    +++ ++   +
Sbjct: 71  VAIDGEPVHFAGPVDAEHRGLVLVHQEILLAPDLTVAQNIFMGRELKRGLMVNDREMNRQ 130

Query: 124 TRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALL 183
           + E +  +G    P T I+ + + ++QLV+IA+AL    +++I DEPTASL   ++EALL
Sbjct: 131 SAEAVHSLGADIDPTTQISRLSIARRQLVQIARALQVPHRVVIFDEPTASLTPFETEALL 190

Query: 184 NLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMVG 243
            ++ + R++G+  + I+H+L EV  +AD+ITVLRDG  + T +    E+    + R MVG
Sbjct: 191 KVIRDLRDKGVAVLYISHRLPEVGAIADRITVLRDGKLIATRNA--SELQPVDMARLMVG 248

Query: 244 RDLEDRYPPR-DVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAG 302
           RD+   YP R D    +T+LEVKN++             D + ++RKGE++G AGL+GAG
Sbjct: 249 RDMSKLYPEREDTTSRQTVLEVKNFDV-------PGYARDASFSLRKGEILGFAGLIGAG 301

Query: 303 RTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNIL 362
           RTE    + G   GH   GD+ ++G PV    VR ++ AG+ Y++EDRK  GL+L  ++ 
Sbjct: 302 RTELFEGLVGLRTGH---GDIKLNGAPVKFHGVRDSMAAGIVYLSEDRKGKGLLLAQDLR 358

Query: 363 HNTTLANLAGVSKASIIDDIKE----MKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVV 418
            N TLA L   +K  +I+  +E     K  SDF  R R R     Q    LSGGNQQK++
Sbjct: 359 TNLTLATLGKFTKGPLIERKREDKSLDKAISDFDIRARRRDLLAGQ----LSGGNQQKLL 414

Query: 419 LSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRI 478
           L+K +   P ++I+DEPTRGID+G K +IY  I  LA  GK V++ISSEM EL+G C RI
Sbjct: 415 LAKMMLLEPSIVIIDEPTRGIDIGTKEQIYKFIASLAKAGKSVVVISSEMQELIGICHRI 474

Query: 479 YVMNEGRIVAELPKGEASQE 498
            VM   RIV E+  GEA  E
Sbjct: 475 LVMRSSRIVGEV-MGEAMTE 493



 Score = 62.4 bits (150), Expect = 4e-14
 Identities = 61/228 (26%), Positives = 99/228 (43%), Gaps = 8/228 (3%)

Query: 278 QVLHDINVTVRKGEVVGIAGLMGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRK 337
           +VL DI++TV  GEV  I G  GAG++     + G     R  G V IDG+PV  +    
Sbjct: 28  EVLTDISLTVMPGEVHAIIGENGAGKSTLMKLMSGHLQPTR--GTVAIDGEPVHFAGPVD 85

Query: 338 AIDAGLAYVTEDRKHLGLVLNDNILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRI 397
           A   GL  V     H  ++L  ++     +     + +  +++D +EM   S        
Sbjct: 86  AEHRGLVLV-----HQEILLAPDLTVAQNIFMGRELKRGLMVND-REMNRQSAEAVHSLG 139

Query: 398 RSSGIFQETVNLSGGNQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAAD 457
                  +   LS   +Q V +++ L     V+I DEPT  +       +  +I  L   
Sbjct: 140 ADIDPTTQISRLSIARRQLVQIARALQVPHRVVIFDEPTASLTPFETEALLKVIRDLRDK 199

Query: 458 GKGVLMISSEMPELLGNCDRIYVMNEGRIVAELPKGEASQESIMRAIM 505
           G  VL IS  +PE+    DRI V+ +G+++A     E     + R ++
Sbjct: 200 GVAVLYISHRLPEVGAIADRITVLRDGKLIATRNASELQPVDMARLMV 247


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: 644
Number of extensions: 35
Number of successful extensions: 11
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: 512
Length of database: 516
Length adjustment: 35
Effective length of query: 477
Effective length of database: 481
Effective search space:   229437
Effective search space used:   229437
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.

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Protein sequences (fasta format)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources