Alignments for a candidate for gguA in Rhodobacter viridis JA737

GapMind for catabolism of small carbon sources

Alignments for a candidate for gguA in Rhodobacter viridis JA737

Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_110806491.1 C8J30_RS14105 sugar ABC transporter ATP-binding protein

Query= TCDB::O05176
         (512 letters)



>NCBI__GCF_003217355.1:WP_110806491.1
          Length = 513

 Score =  387 bits (993), Expect = e-112
 Identities = 208/500 (41%), Positives = 327/500 (65%), Gaps = 16/500 (3%)

Query: 5   ILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEI 64
           ILE+  + K FPGV AL+NV LK++ G +HAL+GENGAGKSTLMK+++GVY      GE+
Sbjct: 22  ILEVDGVRKEFPGVVALDNVQLKIRPGSVHALMGENGAGKSTLMKIIAGVYNPD--RGEV 79

Query: 65  HYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEV-ASNGVISWQQTFNR 123
            + G     R   D+ + GI +IHQEL L+  +++AEN+++  E   + G+I   +    
Sbjct: 80  RFAGEKLVIRTPIDALNCGIAMIHQELNLMNTMTVAENVWIRREPKGAFGLIDHARMGTM 139

Query: 124 TRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALL 183
           T EL   + +   P  ++ D+ V ++Q++EIAKA+S +  +LI+DEPT+++ E++ E L 
Sbjct: 140 TAELFASLNIHLDPLAIVGDLTVAQKQMIEIAKAVSYNSDVLIMDEPTSAITETEVEHLF 199

Query: 184 NLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMVG 243
            ++ + R +G+  + ITHK+NE+ ++AD++TV RDG  + T+     E++ D IIR MVG
Sbjct: 200 AIIRDLRARGVGIVYITHKMNEIFEIADELTVFRDGKYISTVPA--SEVTRDDIIRMMVG 257

Query: 244 RDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAGR 303
           R++ + +P  D PIG+ IL+V+N +          V  +I+  +RKGE++G+AGL+G+GR
Sbjct: 258 REITEMFPKVDCPIGDVILDVQNLSL-------PGVFDNISFKLRKGEILGVAGLVGSGR 310

Query: 304 TEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNILH 363
           +  A ++FG       TGD+ IDG+ V +++ + A+D GLA++TEDRK  G  L  + L 
Sbjct: 311 SNVAEALFGVHPAE--TGDIWIDGEHVVMTSPQVAMDHGLAFLTEDRKETGCFLVLDCLE 368

Query: 364 NTTLANLAG--VSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSK 421
           N  +A +    V+ A  +   +  ++  ++  +LR+++  + +   NLSGGNQQK+++++
Sbjct: 369 NMQMALITRDKVNGAGFVQQAEVTRLVQEYSAKLRVKTPNLAERVENLSGGNQQKLLIAR 428

Query: 422 WLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVM 481
           WL +NP +LILDEPTRGIDVGAK EI+ +I  LA  G  VLMISSE+PE+LG  DRI VM
Sbjct: 429 WLLTNPRILILDEPTRGIDVGAKSEIHRLITALAGQGVAVLMISSELPEVLGMSDRIMVM 488

Query: 482 NEGRIVAELPKGEASQESIM 501
           +EGR+   L + EA+Q  +M
Sbjct: 489 HEGRVSGFLDRAEATQVRVM 508



 Score = 75.5 bits (184), Expect = 4e-18
 Identities = 59/253 (23%), Positives = 119/253 (47%), Gaps = 20/253 (7%)

Query: 258 GETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAGRTEFAMSVFGKSYGH 317
           GE ILEV   +   ++      L ++ + +R G V  + G  GAG++     + G     
Sbjct: 19  GEFILEV---DGVRKEFPGVVALDNVQLKIRPGSVHALMGENGAGKSTLMKIIAGVYNPD 75

Query: 318 RITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNILHNTTLANLAGVSKA- 376
           R  G+V   G+ + + T   A++ G+A + ++          N+++  T+A    + +  
Sbjct: 76  R--GEVRFAGEKLVIRTPIDALNCGIAMIHQEL---------NLMNTMTVAENVWIRREP 124

Query: 377 ----SIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSKWLFSNPDVLIL 432
                +ID  +   + ++    L I    +     +L+   +Q + ++K +  N DVLI+
Sbjct: 125 KGAFGLIDHARMGTMTAELFASLNIHLDPL-AIVGDLTVAQKQMIEIAKAVSYNSDVLIM 183

Query: 433 DEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVMNEGRIVAELPK 492
           DEPT  I       ++ II  L A G G++ I+ +M E+    D + V  +G+ ++ +P 
Sbjct: 184 DEPTSAITETEVEHLFAIIRDLRARGVGIVYITHKMNEIFEIADELTVFRDGKYISTVPA 243

Query: 493 GEASQESIMRAIM 505
            E +++ I+R ++
Sbjct: 244 SEVTRDDIIRMMV 256


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: 618
Number of extensions: 30
Number of successful extensions: 10
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: 513
Length adjustment: 35
Effective length of query: 477
Effective length of database: 478
Effective search space:   228006
Effective search space used:   228006
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