GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pccA in Desulfovibrio vulgaris Miyazaki F

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 8499651 DvMF_0417 pyruvate carboxylase (RefSeq)

Query= SwissProt::I3R7G3
         (601 letters)



>lcl|FitnessBrowser__Miya:8499651 DvMF_0417 pyruvate carboxylase
           (RefSeq)
          Length = 1234

 Score =  317 bits (813), Expect = 1e-90
 Identities = 199/518 (38%), Positives = 288/518 (55%), Gaps = 15/518 (2%)

Query: 5   VLVANRGEIAVRVMRACEE-LGVRTVAVYSEADKHGGHVRYADEAYNIGPARAADSYLDH 63
           +LVANRG  A R+ R+  E      V   ++ DK       A E   +G    A  YLD 
Sbjct: 18  ILVANRGIPARRICRSIRERFDAVAVMTATDIDKTSPAASAAQELLLLGSDPRA--YLDI 75

Query: 64  ESVIEAARKADADAIHPGYGFLAENAEFARKVEDSEFTWVGPSADAMERLGEKTKARSLM 123
           + +I  A++    AIHPG+GF +E+  F  K + +  T++G +A+AM  LG K + R L 
Sbjct: 76  DHIIALAKQRGIVAIHPGWGFASEDERFPAKCKAAGLTFIGSTAEAMNLLGNKVQVRKLA 135

Query: 124 QDADVPVVPGTTEPADSAEDVKAVADDYGYPVAIKAEGGGGGRGLKVVHSEDEVDGQFET 183
           +  D+PVVPG+ E A      + + D+ G PV +KAEGGGGGRG+  +H  +E+   F  
Sbjct: 136 KKLDIPVVPGS-EGAVDIPTARTIIDEIGLPVMLKAEGGGGGRGIFAIHRAEELSDAFMK 194

Query: 184 AKREGEAYFDNASVYVEKYLEAPRHIEVQILADEHGNVRHLGERDCSLQRRHQKVIEEAP 243
           A    +A F N  +YVEKYL + RHIE+Q++AD +GNV    ERDC++QR HQK+IE  P
Sbjct: 195 ASTMAQASFGNPRLYVEKYLPSVRHIEIQVIADMYGNVFAFDERDCTVQRNHQKLIEITP 254

Query: 244 SP--ALSEDLRERIGEAARRGVRAAEYTNAGTVEFLVE-DGEFYFMEVNTRIQVEHTVTE 300
           SP   ++ +LRER+ E +R  VR   Y +  TVEFLV  DG  Y +EVNTR+QVEH +TE
Sbjct: 255 SPWSGITPELRERLKEYSRMLVREVGYHSLCTVEFLVTADGTPYLIEVNTRLQVEHGITE 314

Query: 301 EVTGLDVVKWQLRVAAGEELDFSQDDVEIEGHSMEFRINAEAPEKEFAPATGTLSTYDPP 360
              G+D+V+ Q+ VA G  L F++++   +  +M+ RIN E P+  FAP +G +S Y  P
Sbjct: 315 CRYGIDLVEEQIAVAFGARLRFTEENTTPQHVAMQVRINCEDPQNHFAPNSGLVSRYVSP 374

Query: 361 GGIGIRMDDAVRQGDEIGGDYDSMIAKLIVTGSDREEVLVRAERALNEFDIEGLRTVIPF 420
           GG G+R+D  +  G E   +YDS  + LI  G   E+VL   ER L E+ I G++T +PF
Sbjct: 375 GGPGVRLDSNMCAGYEFPSNYDSAGSLLIAYGQGWEKVLGIMERCLGEYVIGGIKTTVPF 434

Query: 421 HRLMLTDEAFREGSHTTKYLDEVLDPERIEAAVERWSPEAVAGDEEEGEVTERTFTVEVN 480
           ++ +L    FR G   T ++     PE +       +PEA        EV+ + +   V 
Sbjct: 435 YKQVLKHPKFRAGDLDTNFIANT--PELM--CYSDLAPEAERLARLVAEVSAKGYNPYVQ 490

Query: 481 GKRF---EVSLEERGAPAIP-LGGASAAASASKPSGPR 514
              +   E     R  P +P + G    A +  P+G R
Sbjct: 491 LGEYRTRETPRMPRFEPVLPHIPGTVRRAPSPYPTGDR 528


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: 1465
Number of extensions: 74
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: 601
Length of database: 1234
Length adjustment: 42
Effective length of query: 559
Effective length of database: 1192
Effective search space:   666328
Effective search space used:   666328
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 preprint 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