Aligments for a candidate for aacS in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Aligments for a candidate for aacS in Pseudomonas simiae WCS417

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate GFF3324 PS417_17010 AMP-binding protein

Query= reanno::acidovorax_3H11:Ac3H11_3009
         (578 letters)



>FitnessBrowser__WCS417:GFF3324
          Length = 544

 Score =  608 bits (1569), Expect = e-178
 Identities = 303/564 (53%), Positives = 392/564 (69%), Gaps = 28/564 (4%)

Query: 16  SHARGATDVPLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLG 75
           S++RG+ D  L+  TIG  F   VA+ P+ EALV  HQ RRYT+ QL       A A L 
Sbjct: 7   SYSRGSQDKTLLAMTIGQAFDRTVAQFPDGEALVVRHQQRRYTWRQLAETVDLHARAFLA 66

Query: 76  MGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSM 135
           +G+  GDR+GIW+ N AEW + Q+A+A++G++LVNINPAYR++E+EY L + GC+ LV  
Sbjct: 67  LGMQTGDRLGIWAPNCAEWCISQIASAKLGVILVNINPAYRSSELEYVLKQSGCQWLVCA 126

Query: 136 ARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTEL 195
             FKTSDY  ML+ L P+ +G                ++ +D      +  PG L + +L
Sbjct: 127 GSFKTSDYHAMLQALNPDLRG----------------MISLDP-----SPPPGFLPWAQL 165

Query: 196 IARGNAAD-PRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKL 254
            A G      +L      L     +NIQ+TSGTTGFPKGATL+H NILNNG+ +GE + L
Sbjct: 166 AALGTGIPLEQLHSRQTSLHFDQAVNIQYTSGTTGFPKGATLSHHNILNNGYMVGESLGL 225

Query: 255 TPADRLCIPVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVP 314
           T  DRL IPVPLYHCFGMV+GNL C THG T++YPNDGFDPL  L  V +E  TGL+GVP
Sbjct: 226 TAQDRLVIPVPLYHCFGMVMGNLGCITHGTTMIYPNDGFDPLLTLTAVAEEHATGLYGVP 285

Query: 315 TMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVS 374
           TMFIA LDHP+   F+LS+LRTGIMAG+ CP EVM+RV+ +M++ E+ IAYGMTETSPVS
Sbjct: 286 TMFIAMLDHPQLGGFDLSSLRTGIMAGATCPIEVMRRVISEMHMSEVQIAYGMTETSPVS 345

Query: 375 CQSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEA 434
            Q+  D  L +RV+TVG+ QP LE KI+D D G  V  G+ GE CT+GYSVM GYW +  
Sbjct: 346 LQTGADDDLERRVTTVGRTQPQLENKIIDAD-GNTVARGEIGELCTRGYSVMLGYWNNPD 404

Query: 435 KTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQD 494
            TREAID+ GWMHTGDLA+MDA GYV I GR KDM+IRGGEN+YPRE+EEF + HP V D
Sbjct: 405 ATREAIDDAGWMHTGDLASMDAHGYVCIAGRNKDMIIRGGENVYPRELEEFFFTHPAVAD 464

Query: 495 VQVVGVPDQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVT 554
           VQV+G+PD++YGE + AW+   PG    E +++ +CKG+IAH+K P++ +FV  FPMTVT
Sbjct: 465 VQVIGIPDERYGEAIVAWVKFHPGHVANELELQTWCKGRIAHFKTPKHFKFVEEFPMTVT 524

Query: 555 GKIQKFKIRDEMKDQLGLEEQKTA 578
           GKIQKF++R     ++ ++E K A
Sbjct: 525 GKIQKFRMR-----EISIQELKNA 543


Lambda     K      H
   0.320    0.136    0.412 

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: 887
Number of extensions: 36
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: 578
Length of database: 544
Length adjustment: 36
Effective length of query: 542
Effective length of database: 508
Effective search space:   275336
Effective search space used:   275336
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 (21.8 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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 paper from 2022 on GapMind for carbon sources, or view the source code.

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