GapMind for catabolism of small carbon sources

 

Aligments for a candidate for liuB in Caulobacter crescentus NA1000

Align methylcrotonoyl-CoA carboxylase (subunit 2/2) (EC 6.4.1.4) (characterized)
to candidate CCNA_01905 CCNA_01905 urea carboxylase

Query= BRENDA::Q9I299
         (655 letters)



>lcl|FitnessBrowser__Caulo:CCNA_01905 CCNA_01905 urea carboxylase
          Length = 1207

 Score =  403 bits (1036), Expect = e-116
 Identities = 228/437 (52%), Positives = 285/437 (65%), Gaps = 5/437 (1%)

Query: 10  RLLVANRGEIACRVMRSARALGIGSVAVHSDIDRHARHVAEADIAVDLGGAKPADSYLRG 69
           ++L+ANRG IACR++R+ RA+G+ SVAV SD D  + HV+ AD AV LG A  A+SYLR 
Sbjct: 4   KVLIANRGAIACRIIRTLRAMGVKSVAVFSDADAGSLHVSMADEAVRLGPAPAAESYLRA 63

Query: 70  DRIIAAALASGAQAIHPGYGFLSENADFARACEEAGLLFLGPPAAAIDAMGSKSAAKALM 129
           D ++AAA A+GAQAIHPGYGFLSE+A FA+ACE+AG+ F+GP A  I A G K  A+ L 
Sbjct: 64  DLVLAAAQATGAQAIHPGYGFLSESAAFAQACEDAGVTFIGPSADNIRAFGLKHTARDLA 123

Query: 130 EEAGVPLVPGYHGEAQDLETFRREAGRIGYPVLLKAAAGGGGKGMKVVEREAELAEALSS 189
           +  GVPL PG      D       A RIG+PV+LKA AGGGG GM+V E    + EA ++
Sbjct: 124 QAHGVPLAPG-TDLLTDPAAALAAAQRIGFPVILKATAGGGGIGMRVCESAEAVEEAFAA 182

Query: 190 AQREAKAAFGDARMLVEKYLLKPRHVEIQVFADRHGHCLYLNERDCSIQRRHQKVVEEAP 249
            +R A   F D  + +E+Y+ K RH+E+QVF D  G    L ERDCS+QRR+QKVVEE P
Sbjct: 183 VRRLATGNFSDGGVFLERYVHKARHIEVQVFGDGAGRVAALGERDCSLQRRNQKVVEETP 242

Query: 250 APGLGAELRRAMGEAAVRAAQAIGYVGAGTVEFLLD-ERGQFFFMEMNTRLQVEHPVTEA 308
           APGL A  R A+ +AAVR A+A  Y  AGTVEFL D +R  FFF+E+NTRLQVEH VTE 
Sbjct: 243 APGLPAATRTALLDAAVRLAKAANYRSAGTVEFLYDADRDDFFFLEVNTRLQVEHGVTEQ 302

Query: 309 ITGLDLVAWQIRVARGEALPLTQEQVPLNGHAIEVRLYAEDPEGDFLPASGRLMLYREAA 368
           +TG+DLV W +R A G+   L        G AI+VRLYAEDP  D+ P++G L    E A
Sbjct: 303 VTGVDLVEWMVRGAAGDFSFLDTPPPAPRGAAIQVRLYAEDPAQDYRPSAGVL---TEVA 359

Query: 369 AGPGRRVDSGVREGDEVSPFYDPMLAKLIAWGETREEARQRLLAMLAETSVGGLRTNLAF 428
              G R D  V +G EVS FYDPMLAKLI   E R  A   L A L  T + G+ TNL +
Sbjct: 360 FPEGVRADGWVVDGTEVSAFYDPMLAKLIVIAEHRPAAVAALQAALDATRLAGIETNLDW 419

Query: 429 LRRILGHPAFAAAELDT 445
           LR +     F + E+ T
Sbjct: 420 LRTVTRSQPFVSGEVST 436



 Score = 79.7 bits (195), Expect = 7e-19
 Identities = 54/145 (37%), Positives = 79/145 (54%), Gaps = 14/145 (9%)

Query: 515  RRCVRLRHAS--PSQYR-LDGDDLVSRVDGVTRRSAALRRGRQLFLEWE--GELLAIEAV 569
            RR +R+   +   S YR L  ++  S     +RR AA    R    +WE  GE   +EA+
Sbjct: 1056 RRAIRIEEETFRLSDYRRLLAENAESIAAFQSRRQAAFDAERA---DWEAKGEFARVEAL 1112

Query: 570  DPIAEAEAA------HAHQGGLSAPMNGSIVRVLVEPGQTVEAGATLVVLEAMKMEHSIR 623
              +AEA+ A       A    + AP+ G++ +VLVEPGQ VEAGA + ++EAMK E  + 
Sbjct: 1113 SGVAEADDAVAAVEVPAGADLVEAPLGGNVWKVLVEPGQAVEAGAVIAIIEAMKAECDVA 1172

Query: 624  APHAGVVKALYCSEGELVEEGTPLV 648
             P AGVV A+Y   G+ +  G P++
Sbjct: 1173 TPTAGVVSAVYAQPGQPIAAGAPVI 1197



 Score = 28.5 bits (62), Expect = 0.002
 Identities = 17/49 (34%), Positives = 27/49 (55%), Gaps = 1/49 (2%)

Query: 565  AIEAVDPIAEAEAAHAHQGGLSAPMNGSIVRVLVEPGQTVEAGATLVVL 613
            A+EA   IA  EA  A +  ++ P  G +  V  +PGQ + AGA ++ +
Sbjct: 1152 AVEAGAVIAIIEAMKA-ECDVATPTAGVVSAVYAQPGQPIAAGAPVIAV 1199


Lambda     K      H
   0.319    0.135    0.397 

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: 1916
Number of extensions: 82
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 655
Length of database: 1207
Length adjustment: 43
Effective length of query: 612
Effective length of database: 1164
Effective search space:   712368
Effective search space used:   712368
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (26.2 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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