GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aacS in Pseudomonas fluorescens FW300-N1B4

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate Pf1N1B4_3988 Acetoacetyl-CoA synthetase (EC 6.2.1.16) / Long-chain-fatty-acid--CoA ligase (EC 6.2.1.3)

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



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3988 Acetoacetyl-CoA
           synthetase (EC 6.2.1.16) / Long-chain-fatty-acid--CoA
           ligase (EC 6.2.1.3)
          Length = 568

 Score =  621 bits (1602), Expect = 0.0
 Identities = 310/561 (55%), Positives = 400/561 (71%), Gaps = 5/561 (0%)

Query: 16  SHARGATDVPLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLG 75
           S+ RG+ D  L+  TIG  F + VA+ P  EALV  HQ  RYT+ QL       A A L 
Sbjct: 11  SYTRGSQDKALLAMTIGQAFDNTVAQHPNGEALVVRHQQLRYTWQQLSETVDLHARAFLA 70

Query: 76  MGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSM 135
           +GL  GDR+GIW+ N A+W + Q A+A++G++LVNINPAYR++E+EY L + GC+ LV  
Sbjct: 71  LGLQTGDRLGIWAPNCAQWCISQFASAKIGVILVNINPAYRSSELEYVLKQSGCQWLVCA 130

Query: 136 ARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTEL 195
             +KTSDY GML+ L PE   Q  G LQ+ +LP+L+ V+ +D +   G      L  T+L
Sbjct: 131 GAYKTSDYHGMLQGLIPELAEQSIGQLQSERLPELRGVISLDAQPPSGFLPWSQL--TDL 188

Query: 196 IARGNAADPRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLT 255
            A  + +  +L +    L     +NIQ+TSGTTGFPKGATL+H NILNNG+ +GE + LT
Sbjct: 189 AA--SVSIEQLRERQDSLHFDQAVNIQYTSGTTGFPKGATLSHYNILNNGYMVGESLGLT 246

Query: 256 PADRLCIPVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPT 315
             DRL IPVPLYHCFGMV+GNL C THG+T++YPND FDPL  L TV +E+ T L+GVPT
Sbjct: 247 ANDRLVIPVPLYHCFGMVMGNLGCVTHGSTMIYPNDAFDPLLTLSTVAEEKATALYGVPT 306

Query: 316 MFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSC 375
           MFIA LD P+ AEF+LS+LRTGIMAG+ CP EVM+RV+ +M++ E+ IAYGMTETSPVS 
Sbjct: 307 MFIAMLDQPKRAEFDLSSLRTGIMAGATCPIEVMRRVINEMHMSEVQIAYGMTETSPVSL 366

Query: 376 QSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAK 435
           Q+     L  RV+TVG+ QP LE KI+D + G +VP G  GE CT+GYSVM GYW +   
Sbjct: 367 QTGPSDELELRVTTVGRTQPQLESKIID-EAGNLVPRGTIGELCTRGYSVMLGYWNNPQG 425

Query: 436 TREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDV 495
           T EAIDE GWMHTGDLA+M+ EGYV I GR KDM+IRGGENIYPRE+EEF + HP V DV
Sbjct: 426 TAEAIDEAGWMHTGDLASMNDEGYVCIAGRNKDMIIRGGENIYPRELEEFFFTHPAVADV 485

Query: 496 QVVGVPDQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTG 555
           QV+G+P  +YGEE+ AWI   PG   TE +++A+CK +IAH+K PRY +FV  FPMTVTG
Sbjct: 486 QVIGIPCSRYGEEIVAWIKFHPGHSATEQELQAWCKERIAHFKTPRYFKFVEEFPMTVTG 545

Query: 556 KIQKFKIRDEMKDQLGLEEQK 576
           KIQKF++R+   ++L   +++
Sbjct: 546 KIQKFRMREISIEELASTDRQ 566


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: 907
Number of extensions: 33
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: 568
Length adjustment: 36
Effective length of query: 542
Effective length of database: 532
Effective search space:   288344
Effective search space used:   288344
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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