GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ptsG in Caulobacter crescentus NA1000

Align protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized)
to candidate CCNA_00572 CCNA_00572 PTS system, N-acetylglucosamine-specific IIBC component

Query= BRENDA::P69786
         (477 letters)



>FitnessBrowser__Caulo:CCNA_00572
          Length = 582

 Score =  324 bits (831), Expect = 4e-93
 Identities = 194/488 (39%), Positives = 285/488 (58%), Gaps = 32/488 (6%)

Query: 9   LQKVGKSLMLPVSVLPIAGILLGVGSANFSWLPAV----------VSHVMAEAGGSVFAN 58
           LQ +G++LMLP++VLP+A +LL +G  +    PA+          V++    AGG++FA+
Sbjct: 8   LQPLGRALMLPIAVLPVAALLLRIGQPDLLGAPALAAATHGMSLSVANTFGAAGGAIFAS 67

Query: 59  MPLIFAIGVALGFTN-NDGVSALAAVVAYGIMVKTMA--VVAPLVLHLPAEEIA------ 109
           + LIFAIGVA+G    N G + LA VV Y I  K +   +VAP  +   A E A      
Sbjct: 68  LGLIFAIGVAVGLARENHGAAGLAGVVCYVIATKGVEALLVAPPEVAAKAVEGAKDLAIA 127

Query: 110 ---SKHLADTGVLGGIISGAIAAYMFNRFYRIKLPEYLGFFAGKRFVPIISGLAAIFTGV 166
              +K +    +  GI+SG I+  ++NR+  I+LPEYL FF G+RFVPI++GLA +   +
Sbjct: 128 AWKAKEIGKLSIPVGILSGVISGALYNRYSTIQLPEYLAFFGGRRFVPIVAGLAGVVLAL 187

Query: 167 VLSFIWPPIGSAIQTFSQWAAYQNPVVAFGIYGFIERCLVPFGLHHIWNVPFQMQIGEYT 226
           +    W  + + +   S        +    +YG + R L+  GLHHI N      +G++ 
Sbjct: 188 LFGAFWSTLEAGVDGLSGLVTASGDL-GLVVYGLLNRLLIVTGLHHILNNVVWFILGDFN 246

Query: 227 NAAGQVFHGDIPRYMAGDPTAGK-LSGGFLFKMYGLPAAAIAIWHSAKPENRAKVGGIMI 285
              G     D+ R+ AGD TAG  +SG F   M+GLPAA +A+ H+A+PE R  V G++ 
Sbjct: 247 GVTG-----DLNRFAAGDKTAGAFMSGFFPVMMFGLPAACLAMLHTARPERRKAVAGMLG 301

Query: 286 SAALTSFLTGITEPIEFSFMFVAPILYIIHAILAGLAFPICILLGMRDGTSFSHGLIDFI 345
           S ALTSFLTG+TEPIEF+FMF+AP+L+ IHA+L GL+  +  +L ++ G  FS GL D++
Sbjct: 302 SLALTSFLTGVTEPIEFTFMFLAPVLFAIHALLTGLSMALMNMLDVKLGFGFSAGLFDYV 361

Query: 346 VLSGNSSKLWLFPIVGIGYAIVYYTIFRVLIKALDLKTPGRED-ATEDAKATGTSEMAPA 404
           +    +++  L   VG+ Y  +YY +FR  I   DLKTPGRED A   A+A  T     A
Sbjct: 362 LNFNKATRPLLLIPVGLVYGALYYGVFRFAILRFDLKTPGREDEAPPSAQAVTTGGGRGA 421

Query: 405 -LVAAFGGKENITNLDACITRLRVSVADVSKVDQAGLKKLGAAGVV-VAGSGVQAIFGTK 462
            ++AA GG  N+ ++DAC TRLR+ V D   V++  LK LGA GVV  +   +Q + G  
Sbjct: 422 DMLAALGGAANLVSVDACTTRLRLIVVDQGLVNEPALKALGARGVVRPSDKALQVVLGPI 481

Query: 463 SDNLKTEM 470
           +D +  E+
Sbjct: 482 ADTVAGEI 489



 Score = 48.9 bits (115), Expect = 5e-10
 Identities = 30/79 (37%), Positives = 41/79 (51%), Gaps = 1/79 (1%)

Query: 389 ATEDAKATGTSEMAPALVAAFGGKENITNLDACITRLRVSVADVSKVDQAGLKKLGAAG- 447
           A   A A   S+ A AL+AA GG +N+ +L    +RLRV + D  +VDQA L   G  G 
Sbjct: 498 APAPAPAPDVSQAAKALLAALGGADNLRDLSVHASRLRVVLNDPERVDQAALHTAGVRGF 557

Query: 448 VVVAGSGVQAIFGTKSDNL 466
             VA   V  I G  ++ +
Sbjct: 558 AAVAPGAVHIIIGPHAERI 576


Lambda     K      H
   0.325    0.140    0.422 

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: 807
Number of extensions: 55
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: 477
Length of database: 582
Length adjustment: 35
Effective length of query: 442
Effective length of database: 547
Effective search space:   241774
Effective search space used:   241774
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (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