GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gguA in Caulobacter crescentus NA1000

Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate CCNA_00903 CCNA_00903 inositol transport ATP-binding protein IatA

Query= TCDB::O05176
         (512 letters)



>FitnessBrowser__Caulo:CCNA_00903
          Length = 515

 Score =  336 bits (861), Expect = 1e-96
 Identities = 198/507 (39%), Positives = 310/507 (61%), Gaps = 9/507 (1%)

Query: 4   TILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGE 63
           T+L++  ++K+FPGV+AL+ V+L V  GE+HAL+GENGAGKSTL+K+LS  + A    G 
Sbjct: 2   TLLDVSQVSKSFPGVRALDQVDLVVGVGEVHALLGENGAGKSTLIKILSAAHAADA--GT 59

Query: 64  IHYEGAVRNFR-AINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQTFN 122
           + + G V + R A    + +GI  I+QE  L P LS+AEN++LG E    G++ W +   
Sbjct: 60  VTFAGQVLDPRDAPLRRQQLGIATIYQEFNLFPELSVAENMYLGREPRRLGLVDWSRLRA 119

Query: 123 RTRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEAL 182
             + LL  +GL  +P+  +  + V +QQ+VEIAKA++ + +L+I+DEPTA+L+  + + L
Sbjct: 120 DAQALLNDLGLPLNPDAPVRGLTVAEQQMVEIAKAMTLNARLIIMDEPTAALSGREVDRL 179

Query: 183 LNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMV 242
             ++   + + ++ I ++H+L EV+ + D+ TV+RDG  V + D    E+++  ++R MV
Sbjct: 180 HAIIAGLKARSVSVIYVSHRLGEVKAMCDRYTVMRDGRFVASGDVADVEVAD--MVRLMV 237

Query: 243 GRDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAG 302
           GR +E     R  P G  +L+V+       +      L  ++   R GE+VG+AGL+GAG
Sbjct: 238 GRHVEFERRKRRRPPGAVVLKVEGVTPAAPRLSAPGYLRQVSFAARGGEIVGLAGLVGAG 297

Query: 303 RTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNIL 362
           RT+ A  +FG        G VL+D KP+ + + R AI AG+  V EDRK  G  L+ +I 
Sbjct: 298 RTDLARLIFGAD--PIAAGRVLVDDKPLRLRSPRDAIQAGIMLVPEDRKQQGCFLDHSIR 355

Query: 363 HNTTLANLAGVSK-ASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSK 421
            N +L +L  +S     +D+  E  +   +R +LRI+ +        LSGGNQQKV+L +
Sbjct: 356 RNLSLPSLKALSALGQWVDERAERDLVETYRQKLRIKMADAETAIGKLSGGNQQKVLLGR 415

Query: 422 WLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVM 481
            +   P VLI+DEPTRGID+GAK E++ +++ LA  G  V++ISSE+ E++   DRI V 
Sbjct: 416 AMALTPKVLIVDEPTRGIDIGAKAEVHQVLSDLADLGVAVVVISSELAEVMAVSDRIVVF 475

Query: 482 NEGRIVAELPKGEASQESIMRAIMRSG 508
            EG IVA+L    A++E +M A M +G
Sbjct: 476 REGVIVADLDAQTATEEGLM-AYMATG 501


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: 609
Number of extensions: 29
Number of successful extensions: 9
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: 515
Length adjustment: 35
Effective length of query: 477
Effective length of database: 480
Effective search space:   228960
Effective search space used:   228960
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 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