GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuB in Desulfovibrio vulgaris Miyazaki F

Align Methylcrotonyl-CoA carboxylase biotin-containing subunit (EC 6.4.1.4) (characterized)
to candidate 8499651 DvMF_0417 pyruvate carboxylase (RefSeq)

Query= reanno::pseudo1_N1B4:Pf1N1B4_3984
         (651 letters)



>FitnessBrowser__Miya:8499651
          Length = 1234

 Score =  317 bits (812), Expect = 2e-90
 Identities = 190/457 (41%), Positives = 266/457 (58%), Gaps = 7/457 (1%)

Query: 9   LLVANRGEIACRVMRTAKALGLTTVAVHSATDRDARHSREADIRVDLGGSKAADSYLQID 68
           +LVANRG  A R+ R+ +      VAV +ATD D      +  +  L       +YL ID
Sbjct: 18  ILVANRGIPARRICRSIRER-FDAVAVMTATDIDKTSPAASAAQELLLLGSDPRAYLDID 76

Query: 69  KLIAAAKASGAQAIHPGYGFLSENAGFARAIEAAGLIFLGPPASAIDAMGSKSAAKALME 128
            +IA AK  G  AIHPG+GF SE+  F    +AAGL F+G  A A++ +G+K   + L +
Sbjct: 77  HIIALAKQRGIVAIHPGWGFASEDERFPAKCKAAGLTFIGSTAEAMNLLGNKVQVRKLAK 136

Query: 129 TAGVPLVPGYHGEAQDLETFRDACERIGYPVLLKATAGGGGKGMKVVEDVSQLAEALASA 188
              +P+VPG  G A D+ T R   + IG PV+LKA  GGGG+G+  +    +L++A   A
Sbjct: 137 KLDIPVVPGSEG-AVDIPTARTIIDEIGLPVMLKAEGGGGGRGIFAIHRAEELSDAFMKA 195

Query: 189 QREALSSFGDSRMLVEKYLLKPRHVEIQVFADQHGNCLYLNERDCSIQRRHQKVVEEAPA 248
              A +SFG+ R+ VEKYL   RH+EIQV AD +GN    +ERDC++QR HQK++E  P+
Sbjct: 196 STMAQASFGNPRLYVEKYLPSVRHIEIQVIADMYGNVFAFDERDCTVQRNHQKLIEITPS 255

Query: 249 P--GLSPELRRAMGEAAVRSAQAIGYVGAGTVEFLLDARGEFFFMEMNTRLQVEHPVTEA 306
           P  G++PELR  + E +    + +GY    TVEFL+ A G  + +E+NTRLQVEH +TE 
Sbjct: 256 PWSGITPELRERLKEYSRMLVREVGYHSLCTVEFLVTADGTPYLIEVNTRLQVEHGITEC 315

Query: 307 ITGLDLVAWQIRVARGEALPMTQDQVPLIGHAIEVRLYAEDPGNDFLPATGRLALYRESA 366
             G+DLV  QI VA G  L  T++       A++VR+  EDP N F P +G ++ Y  S 
Sbjct: 316 RYGIDLVEEQIAVAFGARLRFTEENTTPQHVAMQVRINCEDPQNHFAPNSGLVSRY-VSP 374

Query: 367 AGPGRRVDSGVEEGDEISPFYDPMLGKLIAWGEDREQARLRLLSMLDEFAIGGLKTNINF 426
            GPG R+DS +  G E    YD     LIA+G+  E+    +   L E+ IGG+KT + F
Sbjct: 375 GGPGVRLDSNMCAGYEFPSNYDSAGSLLIAYGQGWEKVLGIMERCLGEYVIGGIKTTVPF 434

Query: 427 LRRIIGHPAFAAAELDTGFIPRYQEQLLPAPSDLSDE 463
            ++++ HP F A +LDT FI    E  L   SDL+ E
Sbjct: 435 YKQVLKHPKFRAGDLDTNFIANTPE--LMCYSDLAPE 469



 Score = 41.6 bits (96), Expect = 2e-07
 Identities = 29/105 (27%), Positives = 53/105 (50%), Gaps = 7/105 (6%)

Query: 551  DTLYLQWDGELRRIESYDPISAVEASHSHQGGLTAPMNGSIVRVLVEAGQTVEAGAQLVV 610
            D+ ++  + ++ +    D   + +A  S+   + AP NG +  + V  G  V+ G +L  
Sbjct: 1097 DSEFMSCEVQVAKAAVADGKGSEKADPSNPMHVAAPSNGDLWVMYVHPGDVVKQGEELFN 1156

Query: 611  LEAMKMEHSIRAPHAGIIK-----ALYCQEGEM--VSEGSALVEL 648
            +  MK E ++ AP +G++K     A Y +  +M  V EG  +VEL
Sbjct: 1157 ISIMKQEKAVLAPVSGMVKRVLKTADYRESKQMMPVREGELIVEL 1201


Lambda     K      H
   0.318    0.134    0.386 

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: 1693
Number of extensions: 68
Number of successful extensions: 5
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: 651
Length of database: 1234
Length adjustment: 43
Effective length of query: 608
Effective length of database: 1191
Effective search space:   724128
Effective search space used:   724128
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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