GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mglA in Pseudomonas putida KT2440

Align Monosaccharide-transporting ATPase, component of Glucose porter. Also bind xylose (Boucher and Noll 2011). Induced by glucose (Frock et al. 2012). Directly regulated by glucose-responsive regulator GluR (characterized)
to candidate PP_2759 PP_2759 ribose ABC transporter - ATP-binding subunit

Query= TCDB::G4FGN3
         (494 letters)



>FitnessBrowser__Putida:PP_2759
          Length = 512

 Score =  379 bits (974), Expect = e-109
 Identities = 195/493 (39%), Positives = 309/493 (62%), Gaps = 1/493 (0%)

Query: 3   PILEVKSIHKRFPGVHALKGVSMEFYPGEVHAIVGENGAGKSTLMKIIAGVYQPDEGEII 62
           P+LE++ I K F    AL G S+    G VH +VGENGAGKSTL+K++AG+++PD G ++
Sbjct: 4   PVLELRGIVKTFGATRALDGASLRVAAGSVHGLVGENGAGKSTLIKVLAGIHRPDAGSLL 63

Query: 63  YEGRGVRWNHPSEAINAGIVTVFQELSVMDNLSVAENIFMGDEEKRGIFIDYKKMYREAE 122
            +G+      P +    GI  + QE  +    +V E +F G E + G  +D +   REA 
Sbjct: 64  LDGQPHGHFSPRQVERLGIGFIHQERLLPARFTVGEALFFGHERRFGPLLDRRSQQREAA 123

Query: 123 KFMKEEFGIEIDPEEKLGKYSIAIQQMVEIARAVYKKAKVLILDEPTSSLTQKETEKLFE 182
           + + + FG+ +     +G+ S A QQMV+I RA+  K +VL+ DEP+ +L Q+E E+L  
Sbjct: 124 RLLDDYFGLRLPANALIGELSSAEQQMVQIVRALLIKPRVLVFDEPSVALVQREVERLLR 183

Query: 183 VVKSLKEKGVAIIFISHRLEEIFEICDKVSVLRDGEYIGTDSIENLTKEKIVEMMVGRKL 242
           +V+ L++ G+AI++ISH L+EI  +CD+V+VLR+G  +   S  N + E+I  +MV R++
Sbjct: 184 IVQRLRDDGLAIVYISHYLQEIEALCDRVTVLRNGRDVAEVSPRNTSLEQITRLMVNREV 243

Query: 243 EKFYIKEAHEPGEVVLEVKNLSGER-FENVSFSLRRGEILGFAGLVGAGRTELMETIFGF 301
            + Y K A   G ++L+V+ L   R ++ +   +RRGEI+G  GLVG+G  EL+ ++FG 
Sbjct: 244 GELYPKVAVPAGALLLDVRGLGRARAYQGIDLQVRRGEIVGLTGLVGSGAKELLRSLFGL 303

Query: 302 RPKRGGEIYIEGKRVEINHPLDAIEQGIGLVPEDRKKLGLILIMSIMHNVSLPSLDRIKK 361
            P   GE+ ++G+ + +  P +A+ QG+ L+PE+R++ G+ L +S+  N +L +L R  +
Sbjct: 304 APPDSGEVRLDGQPLSLRSPREAVAQGVALMPEERRRQGVALDLSVQENTTLAALSRFVR 363

Query: 362 GPFISFKREKELADWAIKTFDIRPAYPDRKVLYLSGGNQQKVVLAKWLALKPKILILDEP 421
              +S  RE+      I+   I+      KV  LSGGNQQKV LAKW A    + +LDEP
Sbjct: 364 LGLLSPARERHTTLELIERLRIKAHGAHAKVRQLSGGNQQKVALAKWFARCSSLYLLDEP 423

Query: 422 TRGIDVGAKAEIYRIMSQLAKEGVGVIMISSELPEVLQMSDRIAVMSFGKLAGIIDAKEA 481
           + GIDVGAK EIYR++ +L KEG GV+++SS+LPE++ + DRI VM  G +A    A EA
Sbjct: 424 SVGIDVGAKVEIYRLIGELVKEGAGVLILSSDLPELIGLCDRIHVMHRGAIAARFAAGEA 483

Query: 482 SQEKVMKLAAGLE 494
           + ++++ +A G +
Sbjct: 484 NSDRLLAVATGAQ 496


Lambda     K      H
   0.318    0.138    0.385 

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: 601
Number of extensions: 26
Number of successful extensions: 5
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: 494
Length of database: 512
Length adjustment: 34
Effective length of query: 460
Effective length of database: 478
Effective search space:   219880
Effective search space used:   219880
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 (21.7 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