GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccB in Azospirillum thiophilum BV-S

Align Propionyl-CoA carboxylase, carboxyltransferase subunit; PCC; EC 6.4.1.3 (characterized)
to candidate WP_082109125.1 AL072_RS25760 methylmalonyl-CoA carboxyltransferase

Query= SwissProt::I3R7F1
         (516 letters)



>NCBI__GCF_001305595.1:WP_082109125.1
          Length = 531

 Score =  281 bits (718), Expect = 5e-80
 Identities = 173/497 (34%), Positives = 272/497 (54%), Gaps = 24/497 (4%)

Query: 4   EDRIDELREKREEALKGGGEDRIASQHDKGKMTARERIDYFLDDGTFREFDQFRTHRNHK 63
           +D I +L ++ E AL  GG +++A +  KG + ARER+D  LD  +F E   F      +
Sbjct: 27  QDHIQKLHQQTEHALGMGGPEKLAKRRAKGMLNARERLDVLLDPESFWESGMFGRSIRPE 86

Query: 64  FGMEETKLPGDGVITGHGEVDGRTVFVFAHDFTVFGGSLGEVFAEKICKVMDKAMEVGAP 123
            G    K P DG I G+G +DGR V V ++DFTV G S   V  +KI  + + A + G P
Sbjct: 87  MG---EKSPADGKIAGYGRIDGRDVAVVSNDFTVLGASSSAVNGKKIRHMREVASKRGMP 143

Query: 124 VIGLNDSAGARIQEGVQSLGGF------GEIFR-RNTEASGVVPQISAIMGPCAGGAVYS 176
           ++ L +S GAR+ + + + G        GE  R R+T      P  SA++G C G + + 
Sbjct: 144 MVFLGESVGARMPDRMGAPGRAMLGQDPGEYLRDRHT------PWASALLGDCYGSSTWY 197

Query: 177 PALTDFTFMVRDTSHMFITGPDVIKTVTGEEVTFDELGGATTHTSTSGVAHFATDTEEQA 236
             ++DF  M R  + M +    V      E +  ++LGG   H+S +G+     D+EE+A
Sbjct: 198 ACVSDFVVM-RKGATMAVASSRVTSMAISETIDPEDLGGWRLHSSVTGLVDMVVDSEEEA 256

Query: 237 LDDIRHLLSYLPQNNVEDPPRVEPWDDPERVADELEEIVPDQPRKPYDIHDVLNGVLDEG 296
           L  +R  L YLP +  E+ PR    +  +  +D + +++P++  K YD+ DV+N V+D G
Sbjct: 257 LQAVRTFLGYLPSHAGEEAPRRPVPEGSDDASDRILDVLPEERTKVYDVRDVINCVVDTG 316

Query: 297 SFFGVQEDFAKNIVVGFGRLDGHSVGIVANQPRVNAGTLDIEASEKGARFIRFCDSFNIP 356
           SFF ++  F K+I  G  R+DG SVG++A+ PRV  G +D++A  K   F+  CDSFN+P
Sbjct: 317 SFFELKARFGKSITTGLARIDGRSVGVIASNPRVKGGAIDVDAMRKATGFLVLCDSFNLP 376

Query: 357 ILSFVDVPGFLPGTDQEHNGIIRHGAKLLYAYSEATVPLMTVITRKAYGGAY-DVMASKH 415
           I+  VD PGFL G + E           + A S  TVP ++V+ RK+YG AY ++   +H
Sbjct: 377 IVFLVDQPGFLIGVEGERRWAPGRIMNWMNALSLVTVPKLSVLMRKSYGQAYLNMGGGRH 436

Query: 416 LGADVNYAWPTAEIAVMGPQGAVNILYRDELEAADDPDARRDELIEEYREEFANPYTAAD 475
             +D   +WPTA++  + P   VNIL+   ++ +DDP+  R  L +E +++ ++ +  A 
Sbjct: 437 --SDEVLSWPTADLGFVDPAVGVNILH--GIKESDDPERFR-ALYQELQKD-SSAWALAA 490

Query: 476 RGFVDDVIEPGDTRNRL 492
                 VI+P  TR  L
Sbjct: 491 LYETHAVIDPRATRAAL 507


Lambda     K      H
   0.318    0.138    0.407 

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: 665
Number of extensions: 25
Number of successful extensions: 7
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: 516
Length of database: 531
Length adjustment: 35
Effective length of query: 481
Effective length of database: 496
Effective search space:   238576
Effective search space used:   238576
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: 52 (24.6 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