GapMind for catabolism of small carbon sources

 

Alignments 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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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