GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Miya:8499651
          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:

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