GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pccB in Brevibacterium jeotgali SJ5-8

Align Propionyl-CoA carboxylase beta chain; PCCase; Propanoyl-CoA:carbon dioxide ligase; EC 6.4.1.3 (characterized)
to candidate WP_101589346.1 BJEO58_RS10090 acyl-CoA carboxylase subunit beta

Query= SwissProt::P53003
         (546 letters)



>NCBI__GCF_900169175.1:WP_101589346.1
          Length = 536

 Score =  703 bits (1815), Expect = 0.0
 Identities = 362/547 (66%), Positives = 422/547 (77%), Gaps = 12/547 (2%)

Query: 1   MSSATEPVGVPPAEAPDIHTTAGKLADLYRRNHEAVHAGSERAVAKQHAKGKRTARERID 60
           MS  TEP    P ++    TTA ++A  +     A H GSERAVA Q  KGK+TARERID
Sbjct: 1   MSQTTEP---QPPDSSVPRTTADRIA-AFEERRTAAHTGSERAVANQRKKGKQTARERID 56

Query: 61  MLLDEGSFVELDEHARHRSTNFGMDADRPYGDGVVTGWGTVDGRRVCVFSQDFTVFGGSL 120
            LLD GSF E+DE  RH +T+FGM  +RP GDGVV G GT++GR V VF+ DFTV GGSL
Sbjct: 57  QLLDTGSFQEVDEFVRHHNTHFGMMKNRPDGDGVVCGLGTIEGRTVAVFAHDFTVLGGSL 116

Query: 121 GEVFGEKIVKVMDLAMKTGCPLVGINDSGGARIQEGVAALGLYAEIFKRNTHASGVIPQI 180
            E  G KIVKV  LA+K GCP++GINDSGGARIQEGV ++ L+AEIF+ N  +SGVIPQI
Sbjct: 117 AEANGRKIVKVQKLALKLGCPIIGINDSGGARIQEGVGSIALFAEIFRLNVASSGVIPQI 176

Query: 181 SLIMGPCAGGAVYSPAITDFTVMVDQTSHMFITGPDVIKTVTGEDVSFEDLGGARTHNER 240
           SLIMGP AGGAVYSPA+TD T+MVD TSHM+ITGPDVIKTVTGE+V  E+LGG RT+N  
Sbjct: 177 SLIMGPSAGGAVYSPALTDVTIMVDGTSHMYITGPDVIKTVTGENVGHEELGGGRTNNTV 236

Query: 241 SGNAHYLATDEDDAISYVKELLSFLPSNNLSSSPVFPG-AEVEEGSVADGVGDADLELDA 299
           +GNAHYLA DE DAI YV++LLS+LP N+L   P +   A +EE        + D  LDA
Sbjct: 237 TGNAHYLAEDEPDAIDYVRDLLSYLPQNSLDPVPRYDEPAHLEES-------EEDRALDA 289

Query: 300 LVPDSPNQPYDMREVITRLVDEGEFLEVSALFAPNMLCGFGRIEGASVGVVANQPMQLAG 359
           LVPDSP+QPYD+  V+  ++D    L+VS LFAPN++  FGR+EG SVG++ANQPMQLAG
Sbjct: 290 LVPDSPSQPYDILRVVEAVLDPETLLQVSELFAPNVVTAFGRVEGRSVGIIANQPMQLAG 349

Query: 360 TLDIDASEKAARFVRFCDAFNIPVLTLVDVPGFLPGTGQEWNGIIRRGAKLLYAYAEATV 419
           TLDIDASEKAARFVR CDAFNIP+LT VDVPGFLPGT QE+ GIIRRGAKL+YAY EATV
Sbjct: 350 TLDIDASEKAARFVRLCDAFNIPILTFVDVPGFLPGTDQEYGGIIRRGAKLIYAYGEATV 409

Query: 420 PLVTVITRKAYGGAYDVMGSKHLGADINLAWPTAQIAVMGAQGAANILYRRQLAEAAERG 479
           PLVT+ITRKAYGGAY VMGSK LGADINLAWP+AQIAVMGAQGAANI+YRR LA   E G
Sbjct: 410 PLVTLITRKAYGGAYCVMGSKQLGADINLAWPSAQIAVMGAQGAANIVYRRDLAAVDEAG 469

Query: 480 EDVEALRARLQQEYEDTLCNPYVAAERGYVDSVIPPSHTRGHVARALRMLADKREALPAK 539
            DV+A R  L QEYED L NPY+AAE GY+D+VI PS TR  + R+LR L +K    PA+
Sbjct: 470 GDVDARREELIQEYEDALLNPYLAAEEGYIDAVIRPSETRERIVRSLRALENKHVEQPAR 529

Query: 540 KHGNIPL 546
           KHGNIPL
Sbjct: 530 KHGNIPL 536


Lambda     K      H
   0.318    0.136    0.398 

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: 862
Number of extensions: 31
Number of successful extensions: 3
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: 546
Length of database: 536
Length adjustment: 35
Effective length of query: 511
Effective length of database: 501
Effective search space:   256011
Effective search space used:   256011
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