Alignments for a candidate for aacS in Belnapia rosea CPCC 100156

GapMind for catabolism of small carbon sources

Alignments for a candidate for aacS in Belnapia rosea CPCC 100156

Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_090664130.1 BLR02_RS17730 AMP-binding protein

Query= BRENDA::Q9Z3R3
         (650 letters)



>NCBI__GCF_900101615.1:WP_090664130.1
          Length = 625

 Score =  149 bits (376), Expect = 4e-40
 Identities = 178/632 (28%), Positives = 259/632 (40%), Gaps = 54/632 (8%)

Query: 44  WSVSERGAFWTAVWEHCKVIGESGEKALVDGDRMLDARFFPEARLNFAENLLRK---TGS 100
           W  + RG  W           E    A+ D    +  R+FP+ARLN   N L +    G 
Sbjct: 19  WREAARGIDW-----------ERAPAAIFDPKAGVYGRWFPDARLNTCHNALDRHVAAGR 67

Query: 101 GDALIFRGEDKVSYR---LTWDELRALVSRLQQALRAQGIGAGDRVAAMMPNMPETIALM 157
           G       +  V+ R    T+DEL A V++L  AL A+GI AGDRV   +P +PE    M
Sbjct: 68  GAQPALHYDSPVTGRSRSFTYDELLARVAKLAGALAARGIAAGDRVVIYLPMVPEAAIAM 127

Query: 158 LATASVGAIWSSCSPDFGEQGVLDRFGQIAPKLFIVCDGYWYNGKRQDVDSKVRAVAKSL 217
           LA A +GA+ S     F    +  R     PKL I        G       +V A    L
Sbjct: 128 LACARLGAVHSVVFGGFAAAELAARIADARPKLVISASCGIEPG-------RVVAYKPLL 180

Query: 218 GAPTVIVPYAGDSAALAPTVEGGVTLA-----DFI-AGFQAGPLVFERLPFGHPLYILFS 271
            A   + P+  D   +    E   TL      D + A   A P     +    PLYIL++
Sbjct: 181 DAAIGLSPHKPDHCLILRRPELDCTLTPGRDEDLLEAEAAATPHPCVPVAATDPLYILYT 240

Query: 272 SGTTGVPKCIVHSAGGTLLQHLKEHRFHCGLRDGERLFYFTTCGWMMWN--WLASGLAVG 329
           SGTTG PK +V   GG  +      R   GL  G+ +F  +  GW++ +   + + L  G
Sbjct: 241 SGTTGKPKGVVRDNGGHAVALHNSMRMLYGLGAGDVMFTASDVGWVVGHSYIVYAPLLAG 300

Query: 330 ATLCLYDGSPF-CPDGNVLFDYAAAERFAVFGTSAKYIDAVRK---GGFTPARTHDLSSL 385
           AT  LY+G P   PD +  +   A  R     T+   + A+++    G   A  HDLS+L
Sbjct: 301 ATTVLYEGKPVGTPDASAFWRVCAQYRVTAMFTAPTAMRAIKREDPEGRLMA-GHDLSAL 359

Query: 386 RLMTSTGSPLSPEGFSFVYEGIKPDV--QLASISGGTDIVSCFVLGNPLKPVWRGEIQGP 443
           + +   G    P    +    ++  V         G  I   F      +P + G    P
Sbjct: 360 QALFLAGERCDPPTAEWAAGLLRRPVIDHWWQTETGWAITGNFRGLGLFEPRF-GSGGKP 418

Query: 444 GLGLAVDVWNDEGKP-VRGEKGELVCTRAFP--SMPVMFWNDPDGAKYRAAYFDRFDNVW 500
             G  V   +D G+P   GE G L      P   +P + W   D  + R AY + F   +
Sbjct: 419 SPGYEVAALDDAGQPQPPGETGTLAIRLPMPPGCLPTL-WQADD--RCREAYLEAFPGWY 475

Query: 501 CHGDFAEWTPHGGIVIHGRSDATLNPGGVRIGTAEIYNQVEQMDEVAEALCIGQDWEDDV 560
              D       G + +  R+D  +N  G R+ T  +   +    +VAE   +G       
Sbjct: 476 NTSDAGVIDADGYVSVMSRTDDIINVAGHRLSTGAMEEVLAGHPDVAECAVLGVKDSLKG 535

Query: 561 RVVL-FVRLARGVELTEA-LTREIKNRIRSGASPRHVPAKIIAVADIPRTKSGKIVELAV 618
           +V L  V L  GV   EA L RE+   +R    P         V  +P+T+SGKI+   +
Sbjct: 536 QVPLGLVVLKSGVARPEADLARELVALVRERIGPVAAFKDAKVVTRLPKTRSGKILRATL 595

Query: 619 RDVVHGRPVKNKEALANPEALDLFAGLEELKS 650
           R +  G      E+ A P  +D  A LEE+++
Sbjct: 596 RKIADG------ESYAVPPTIDDPAILEEMQA 621


Lambda     K      H
   0.322    0.139    0.441 

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: 1114
Number of extensions: 61
Number of successful extensions: 6
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: 650
Length of database: 625
Length adjustment: 38
Effective length of query: 612
Effective length of database: 587
Effective search space:   359244
Effective search space used:   359244
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (25.4 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources