GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccA1 in Rhodobacter ovatus JA234

Align acyl CoA carboxylase biotin carboxylase subunit (EC 2.1.3.15; EC 6.4.1.3; EC 6.3.4.14) (characterized)
to candidate WP_097029448.1 CRO07_RS04350 pyruvate carboxylase

Query= metacyc::MONOMER-13597
         (509 letters)



>NCBI__GCF_900207575.1:WP_097029448.1
          Length = 1154

 Score =  349 bits (895), Expect = e-100
 Identities = 188/460 (40%), Positives = 281/460 (61%), Gaps = 9/460 (1%)

Query: 1   MPPFSRVLVANRGEIATRVLKAIKEMGMTAIAVYSEADKYAVHTKYADEAYYIGKAPA-L 59
           M  F ++L+ANRGEIA RV++A  EMG   +AVY+E DK ++H   ADEAY IG+  + +
Sbjct: 1   MAEFRKILIANRGEIAIRVMRAANEMGKKTVAVYAEEDKLSLHRFKADEAYRIGEGLSPV 60

Query: 60  DSYLNIEHIIDAAEKAHVDAIHPGYGFLSENAEFAEAVEKAGITFIGPSSEVMRKIKDKL 119
            +YL+I  II  A+ +  DAIHPGYG LSEN +F EA + AGI FIGP +E MR + DK 
Sbjct: 61  GAYLSIPEIIRVAKMSGADAIHPGYGLLSENPDFVEACDAAGIAFIGPRAETMRALGDKA 120

Query: 120 DGKRLANMAGVPTAPGSDGPVTSIDEALKLAEKIGYPIMVKAASGGGGVGITRVDNQDQL 179
             +R+A  AGVP  P ++     +DE  + A ++GYP+M+KA+ GGGG G+  + ++ +L
Sbjct: 121 SARRVAMAAGVPVIPATEVLGDDMDEVKRQAAEVGYPLMLKASWGGGGRGMRPIPSEAEL 180

Query: 180 MDVWERNKRLAYQAFGKADLFIEKYAVNPRHIEFQLIGDKYGNYVVAWERECTIQRRNQK 239
            D     +R A  AFG  + ++EK  +  RH+E Q++GDK GN    +ER+CT+QRRNQK
Sbjct: 181 ADKVREGRREAEAAFGNGEGYLEKMILRARHVEVQILGDKQGNIYHLYERDCTVQRRNQK 240

Query: 240 LIEEAPSPALKMEERESMFEPIIKFGKLINYFTLGTFETAFSDVSRDFYFLELNKRLQVE 299
           ++E AP+P L  ++R  + E   +    +NY   GT E      S+ FYF+E+N R+QVE
Sbjct: 241 VVERAPAPYLTDDQRAEVCELGRRICAHVNYECAGTVEFLMDMDSQQFYFIEVNPRVQVE 300

Query: 300 HPTTELIFRIDLVKLQIKLAAGEHLPFS-----QEDLNKRVRGTAIEYRINAEDALNNFT 354
           H  TE +  ID+V+ QI++A G  L  +     QED+   + G A++ R+  ED  NNF 
Sbjct: 301 HTVTEEVTGIDIVQAQIRIAEGATLAEATGVARQEDIT--LSGHALQCRVTTEDPQNNFI 358

Query: 355 GSSGFVTYYREPTGPGVRVDSGIE-SGSYVPPYYDSLVSKLIVYGESREYAIQAGIRALA 413
              G +T YR  TG G+R+D G   +G  +  YYDSL+ K+  + ++ E AI    RAL 
Sbjct: 359 PDYGRLTAYRSATGMGIRLDGGTAYAGGVITRYYDSLLVKVTAWAQTPEKAISRMDRALR 418

Query: 414 DYKIGGIKTTIELYKWIMQDPDFQEGKFSTSYISQKTDQF 453
           +++I G+ T I   + +++ P F +  ++T +I    + F
Sbjct: 419 EFRIRGVATNIAFVENLLKHPSFLDYSYTTKFIDTTPELF 458


Lambda     K      H
   0.317    0.135    0.385 

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: 1151
Number of extensions: 46
Number of successful extensions: 4
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: 509
Length of database: 1154
Length adjustment: 40
Effective length of query: 469
Effective length of database: 1114
Effective search space:   522466
Effective search space used:   522466
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 (21.6 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Sep 24 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