GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pccA in Magnetospirillum magneticum AMB-1

Align Propionyl-CoA carboxylase, biotin carboxylase and biotin-carboxyl carrier subunit; PCC; EC 6.4.1.3; EC 6.3.4.14 (characterized)
to candidate WP_011382686.1 AMB_RS01215 pyruvate carboxylase

Query= SwissProt::I3R7G3
         (601 letters)



>lcl|NCBI__GCF_000009985.1:WP_011382686.1 AMB_RS01215 pyruvate
           carboxylase
          Length = 1154

 Score =  374 bits (961), Expect = e-108
 Identities = 208/452 (46%), Positives = 280/452 (61%), Gaps = 12/452 (2%)

Query: 2   FSKVLVANRGEIAVRVMRACEELGVRTVAVYSEADKHGGHVRYADEAYNIGPARAA-DSY 60
           F+K+LVANRGEIA+R+ RA  ELG+ TVAVYS  D+   H   ADE+Y IG  +   ++Y
Sbjct: 11  FAKLLVANRGEIAIRICRAATELGLATVAVYSTEDRFALHRFKADESYLIGKGKGPIEAY 70

Query: 61  LDHESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKAR 120
           L  + +I   ++A  DA+HPGYGFL+EN +FA  V  +   +VGPS+D M  LG K  AR
Sbjct: 71  LSIDEMIRVGKEAGCDAVHPGYGFLSENPDFADAVRAAGMAFVGPSSDVMRLLGNKVAAR 130

Query: 121 SLMQDADVPVVPGTTE-PADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDG 179
           +L + A VPV+P T   PAD  E  K  A   GYP+ +KA  GGGGRG++V+ +E E++ 
Sbjct: 131 ALAEKAGVPVMPATGPLPADLVE-CKRQAAAVGYPLMLKASWGGGGRGMRVIEAETELEE 189

Query: 180 QFETAKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVI 239
               A+RE +A F N  VY+EK +   RH+EVQIL D  GN+ HL ERDCS+QRR+QKV+
Sbjct: 190 LLAVARREAKAAFGNDEVYLEKLVRRARHVEVQILGDSQGNLVHLYERDCSVQRRNQKVV 249

Query: 240 EEAPSPALSEDLRERIGEAARRGVRAAEYTNAGTVEFL--VEDGEFYFMEVNTRIQVEHT 297
           E AP+P L    R  + E A R  RAA Y NAGTVEFL  +E G FYF+EVN R+QVEHT
Sbjct: 250 ERAPAPYLDGRQRSELCETAVRLARAAAYENAGTVEFLMDMETGAFYFIEVNPRVQVEHT 309

Query: 298 VTEEVTGLDVVKWQLRVAAGEELDF------SQDDVEIEGHSMEFRINAEAPEKEFAPAT 351
           VTE VTG+D+VK Q+R+A G  +         Q ++ + GH+++ RI  E P   F P  
Sbjct: 310 VTEVVTGIDIVKAQIRIAGGAPIGAPGSDVPKQAEIPLNGHAIQCRITTEDPANNFIPDY 369

Query: 352 GTLSTYDPPGGIGIRMDDAVR-QGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFD 410
           G +S Y    G GIR+D      G  I   YDS++ K+       EE + R +RAL EF 
Sbjct: 370 GRISAYRGANGFGIRLDGGTAFSGALITRYYDSLLEKVTAWAPTPEEAIARMDRALREFR 429

Query: 411 IEGLRTVIPFHRLMLTDEAFREGSHTTKYLDE 442
           I G+ T + F   ++    F   ++TT+++DE
Sbjct: 430 IRGVATNLTFLEAVIEHPKFVGCAYTTRFIDE 461



 Score = 57.4 bits (137), Expect = 3e-12
 Identities = 47/157 (29%), Positives = 75/157 (47%), Gaps = 29/157 (18%)

Query: 444  LDPERIEAAVERWSPEAVAGDEEEGEVTERTFTVEVNGKRFEVSLEERGAPAIPLGGASA 503
            +D E+ ++ + R+   A A  EE+G    R    E+NG+   V + +R           A
Sbjct: 1025 IDLEKGKSLIVRYLATAEA--EEDGS---RKVFFELNGQPRTVRVFDRKV---------A 1070

Query: 504  AASASKPSGPRKRREESDEGGQQVIEGDGESVAAEMQGTILAVEVDEGDDVEPGDTVCIL 563
             A A++P                   G+ + V A M G +++V V  G  V+ GD +  +
Sbjct: 1071 PARAARPKAEA---------------GNADHVGAPMPGLVVSVAVHAGQAVDKGDLLVSI 1115

Query: 564  EAMKMENDVVAERGGTVSQVLVGEGDSVDMGDVLLVL 600
            EAMKME  V A+R GTV+ V V  G  V+  D+L+++
Sbjct: 1116 EAMKMETAVRADRAGTVASVAVTPGVQVEAKDLLVIM 1152


Lambda     K      H
   0.312    0.132    0.371 

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: 1362
Number of extensions: 62
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: 2
Length of query: 601
Length of database: 1154
Length adjustment: 42
Effective length of query: 559
Effective length of database: 1112
Effective search space:   621608
Effective search space used:   621608
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (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