GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ptsG-crr in Caulobacter crescentus NA1000

Align PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized)
to candidate CCNA_00458 CCNA_00458 PTS system, N-acetylglucosamine-specific IIBC component

Query= CharProtDB::CH_001857
         (699 letters)



>FitnessBrowser__Caulo:CCNA_00458
          Length = 584

 Score =  368 bits (945), Expect = e-106
 Identities = 221/539 (41%), Positives = 321/539 (59%), Gaps = 35/539 (6%)

Query: 8   VLQKIGRALMLPVAILPAAGILLAIG--NAMQNKDMIQVLHFLSNDNVQLVAGVMESAGQ 65
           +LQ +GRALMLP+A+LP A +LL IG  + +    +    H +S      VA    +AG 
Sbjct: 7   ILQPLGRALMLPIAVLPVAALLLRIGQPDLLGAPALAAATHGMSLS----VANTFGAAGG 62

Query: 66  IVFDNLPLLFAVGVAIGLANGD-GVAGIAAIIGYLVMNVSMSAVLLANGTIPSDSVERAK 124
            +F +L L+FA+GVA+GLA  + G AG+A ++ Y++    + A+L+A   + + +VE AK
Sbjct: 63  AIFASLGLIFAIGVAVGLARENHGAAGLAGVVCYVIATKGVEALLVAPPEVAAKAVEGAK 122

Query: 125 --FFTENHPAYVNMLGIPTLATGVFGGIIVGVLAALLFNRFYTIELPQYLGFFAGKRFVP 182
                      +  L IP        GI+ GV++  L+NR+ TI+LP+YL FF G+RFVP
Sbjct: 123 DLAIAAWKAKEIGKLSIPV-------GILSGVISGALYNRYSTIQLPEYLAFFGGRRFVP 175

Query: 183 IVTSISALILGLIMLVIWPPIQHGLNAFSTGLVEANPTLAAFIFGVIERSLIPFGLHHIF 242
           IV  ++ ++L L+    W  ++ G++  S GLV A+  L   ++G++ R LI  GLHHI 
Sbjct: 176 IVAGLAGVVLALLFGAFWSTLEAGVDGLS-GLVTASGDLGLVVYGLLNRLLIVTGLHHIL 234

Query: 243 YSPFWYEFFSYKSAAGEIIRGDQRIFMAQIKDGVQLTAGTFMTGKYPFMMFGLPAAALAI 302
            +  W+    +    G++ R     F A  K     TAG FM+G +P MMFGLPAA LA+
Sbjct: 235 NNVVWFILGDFNGVTGDLNR-----FAAGDK-----TAGAFMSGFFPVMMFGLPAACLAM 284

Query: 303 YHEAKPQNKKLVAGIMGSAALTSFLTGITEPLEFSFLFVAPVLFAIHCLFAGLSFMVMQL 362
            H A+P+ +K VAG++GS ALTSFLTG+TEP+EF+F+F+APVLFAIH L  GLS  +M +
Sbjct: 285 LHTARPERRKAVAGMLGSLALTSFLTGVTEPIEFTFMFLAPVLFAIHALLTGLSMALMNM 344

Query: 363 LNVKIGMTFSGGLIDYFLFGILPNRTAWWLVIPVGLGLAVIYYFGFRFAIRKFNLKTPGR 422
           L+VK+G  FS GL DY L       T   L+IPVGL    +YY  FRFAI +F+LKTPGR
Sbjct: 345 LDVKLGFGFSAGLFDYVL--NFNKATRPLLLIPVGLVYGALYYGVFRFAILRFDLKTPGR 402

Query: 423 EDAAEETAAPGKTGEAGDLPYEILQAMGDQENIKHLDACITRLRVTVNDQKKVDKDRLKQ 482
           ED A  +A    TG  G    ++L A+G   N+  +DAC TRLR+ V DQ  V++  LK 
Sbjct: 403 EDEAPPSAQAVTTG--GGRGADMLAALGGAANLVSVDACTTRLRLIVVDQGLVNEPALKA 460

Query: 483 LGASGVLEVGNN-IQAIFGPRSDGLKTQMQDIIAGRKPRPEPKTSAQEEVGQQVEEVIA 540
           LGA GV+   +  +Q + GP +D +  +++  I+     P P  +   +V Q  + ++A
Sbjct: 461 LGARGVVRPSDKALQVVLGPIADTVAGEIRHAISA---PPAPAPAPAPDVSQAAKALLA 516



 Score = 44.3 bits (103), Expect = 2e-08
 Identities = 24/91 (26%), Positives = 44/91 (48%), Gaps = 1/91 (1%)

Query: 425 AAEETAAPGKTGEAGDLPYEILQAMGDQENIKHLDACITRLRVTVNDQKKVDKDRLKQLG 484
           +A    AP    +       +L A+G  +N++ L    +RLRV +ND ++VD+  L   G
Sbjct: 494 SAPPAPAPAPAPDVSQAAKALLAALGGADNLRDLSVHASRLRVVLNDPQRVDQAALHTAG 553

Query: 485 ASGVLEVGNN-IQAIFGPRSDGLKTQMQDII 514
             G + VG +    + GP +  +   ++ +I
Sbjct: 554 VRGFVRVGEHAAHVVLGPEAQRIGQAVRAMI 584


Lambda     K      H
   0.323    0.141    0.412 

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: 1096
Number of extensions: 62
Number of successful extensions: 8
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: 699
Length of database: 584
Length adjustment: 38
Effective length of query: 661
Effective length of database: 546
Effective search space:   360906
Effective search space used:   360906
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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