GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3988
          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:

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