GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gguA in Rhodobacter johrii JA192

Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate WP_069332735.1 C8J29_RS16570 sugar ABC transporter ATP-binding protein

Query= TCDB::O05176
         (512 letters)



>NCBI__GCF_003046325.1:WP_069332735.1
          Length = 499

 Score =  335 bits (860), Expect = 2e-96
 Identities = 192/505 (38%), Positives = 298/505 (59%), Gaps = 15/505 (2%)

Query: 1   MANTILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTY 60
           M   +L +R +++ F  V+ L +V+  ++ GE+HAL+GENGAGKST MK+L+G       
Sbjct: 1   MTEPVLAIRQVSRLFGPVQVLFDVDFDLRPGEVHALIGENGAGKSTTMKILAGYLAPSA- 59

Query: 61  EGEIHYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQT 120
            GE+  +G   +F +  ++E  G+++IHQE  L   L++ ENIFLG E+     +  +  
Sbjct: 60  -GEVLLDGRPVHFPSSREAEAAGVVMIHQEFNLATPLTVEENIFLGRELKRGPFLDHRAM 118

Query: 121 FNRTRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSE 180
              +R LL+++     P   ++ + V  +Q+VEIAKAL    ++LI+DEPTA L   +++
Sbjct: 119 QAESRRLLERLHCAVDPRARVSTLSVPNRQMVEIAKALGLKARVLIMDEPTAVLTHRETD 178

Query: 181 ALLNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRN 240
            LL  +   R  G   +  +HKL+EV ++AD++TVLRDG  V T     + +SED +   
Sbjct: 179 TLLEQVDRLRAAGTAILYTSHKLDEVARIADRVTVLRDGRRVMTAPA--KGLSEDRMAET 236

Query: 241 MVGRDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMG 300
           MVGR+L   +PP+  P  E +LEV               + D + T+R+GEV+G AGL+G
Sbjct: 237 MVGRELSGLFPPKSSPAPEPVLEVAGLTV-------PGFVRDASFTLRRGEVLGFAGLVG 289

Query: 301 AGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDN 360
           +GRTE    + G       TG+V ++G P+  ++V  A  AGL Y+TEDRK  GL+L   
Sbjct: 290 SGRTELMEGIVGL---RPATGEVRMEGSPLPHASVSAARAAGLVYLTEDRKEKGLLLGKP 346

Query: 361 ILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLS 420
           +  N TL  L    +  +ID   E +  +   +   IR         +LSGGNQQK++L+
Sbjct: 347 LGENLTLLALDRFGRV-LIDKAAEERALTQAISDFDIRVGDRGISAGSLSGGNQQKLLLA 405

Query: 421 KWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYV 480
           K + + P V+I+DEPTRGIDVG K +IY  I +LAA+G+ V+++SSE+PE++G  +R+ V
Sbjct: 406 KTMLAEPRVVIIDEPTRGIDVGTKQQIYGFIARLAAEGRSVIVVSSELPEVIGLANRVVV 465

Query: 481 MNEGRIVAELPKGEASQESIMRAIM 505
           M+ GRI  E+     ++E+I+R  M
Sbjct: 466 MSAGRIAGEVEGEAITEENIVRLAM 490


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: 597
Number of extensions: 38
Number of successful extensions: 12
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: 499
Length adjustment: 34
Effective length of query: 478
Effective length of database: 465
Effective search space:   222270
Effective search space used:   222270
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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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