Alignments for a candidate for gguA in Trichormus variabilis ATCC 29413

GapMind for catabolism of small carbon sources

Alignments for a candidate for gguA in Trichormus variabilis ATCC 29413

Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_011318959.1 AVA_RS10980 sugar ABC transporter ATP-binding protein

Query= TCDB::O05176
         (512 letters)



>NCBI__GCF_000204075.1:WP_011318959.1
          Length = 517

 Score =  366 bits (939), Expect = e-105
 Identities = 204/504 (40%), Positives = 315/504 (62%), Gaps = 17/504 (3%)

Query: 2   ANTILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYE 61
           A  +LEM+ I K F GV AL+ VNL +  GE+HAL+GENGAGKSTLMK+L+G Y A   E
Sbjct: 15  ATPVLEMQGIAKRFHGVPALQGVNLTIYPGEVHALMGENGAGKSTLMKILAGAYIAD--E 72

Query: 62  GEIHYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQTF 121
           GEI   G          +   GI +I+QEL + P L++ ENIF+G+E+     +  +   
Sbjct: 73  GEIRINGKGVKITDPGTARQAGINLIYQELNVAPNLTVTENIFMGSELTRGQFLDRKAME 132

Query: 122 NRTRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEA 181
              +++L  +G   +P  ++  + + +QQ VEIA+AL  + ++L++DEPTA+L++ ++E 
Sbjct: 133 LEAQQVLASLGASFAPTDIVGTLAIAEQQQVEIARALKDNSRILVMDEPTAALSDRETER 192

Query: 182 LLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNM 241
           L  ++ + RN G+  I I+H++ E+  +AD+I+VLRDG  + +L   +EEIS   +++ M
Sbjct: 193 LFEVIRKLRNDGIAIIYISHRMEEIYALADRISVLRDGQYIGSLT--REEISPQRLVQMM 250

Query: 242 VGRDLEDRYP-PRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMG 300
           VGR ++D Y   R    G  +LEV+N +       D + +   +  +R GE++G+AGL+G
Sbjct: 251 VGRSMQDFYEHQRQSNPGPVVLEVRNIS-------DGRKVQPASFQLRAGEILGLAGLVG 303

Query: 301 AGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDN 360
           AGRTE +  +FG     +++G+V ++GK +++ +   AI  G+ YV EDRK  GL L  +
Sbjct: 304 AGRTEVSRLIFGAD--RKVSGEVFLNGKKLEIHSPSDAIAVGIGYVPEDRKDQGLFLEMS 361

Query: 361 ILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLS 420
              N  L  L   +   I++     K+A+D      IR + +    V+LSGGNQQK++L+
Sbjct: 362 SRKNIGLNRLKQDANLGIVNWGSVNKIATDAVENFHIRLANLEIRAVDLSGGNQQKLLLA 421

Query: 421 KWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYV 480
           +WL  NP VL+LDEPTRG+D+GAK EIY II+ L+A G  +LM+SSE+PE++G  DR+ V
Sbjct: 422 RWLAINPRVLMLDEPTRGVDIGAKSEIYRIISDLSAQGVAILMVSSELPEIVGLSDRVLV 481

Query: 481 MNEGRIVAELPKG---EASQESIM 501
           M EG++V EL      E +QE+IM
Sbjct: 482 MREGQLVGELDNSIGKEITQENIM 505



 Score = 72.8 bits (177), Expect = 3e-17
 Identities = 54/231 (23%), Positives = 108/231 (46%), Gaps = 18/231 (7%)

Query: 280 LHDINVTVRKGEVVGIAGLMGAGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAI 339
           L  +N+T+  GEV  + G  GAG++     + G        G++ I+GK V ++    A 
Sbjct: 34  LQGVNLTIYPGEVHALMGENGAGKSTLMKILAGAYIADE--GEIRINGKGVKITDPGTAR 91

Query: 340 DAGLAYVTEDRKHL-GLVLNDNILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIR 398
            AG+  + ++      L + +NI   + L      ++   +D     + A +   +  + 
Sbjct: 92  QAGINLIYQELNVAPNLTVTENIFMGSEL------TRGQFLD-----RKAMELEAQQVLA 140

Query: 399 SSGIFQETVNLSG----GNQQKVVLSKWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQL 454
           S G      ++ G      QQ+V +++ L  N  +L++DEPT  +       ++ +I +L
Sbjct: 141 SLGASFAPTDIVGTLAIAEQQQVEIARALKDNSRILVMDEPTAALSDRETERLFEVIRKL 200

Query: 455 AADGKGVLMISSEMPELLGNCDRIYVMNEGRIVAELPKGEASQESIMRAIM 505
             DG  ++ IS  M E+    DRI V+ +G+ +  L + E S + +++ ++
Sbjct: 201 RNDGIAIIYISHRMEEIYALADRISVLRDGQYIGSLTREEISPQRLVQMMV 251


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: 648
Number of extensions: 33
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 512
Length of database: 517
Length adjustment: 35
Effective length of query: 477
Effective length of database: 482
Effective search space:   229914
Effective search space used:   229914
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 Apr 09 2024. 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:

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