GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Pseudomonas putida KT2440

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate PP_3458 PP_3458 Butyrate--CoA ligase

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



>FitnessBrowser__Putida:PP_3458
          Length = 562

 Score =  625 bits (1611), Expect = 0.0
 Identities = 309/556 (55%), Positives = 395/556 (71%), Gaps = 7/556 (1%)

Query: 16  SHARGATDVPLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLG 75
           S+ +G  D PL+ Q IG  F   VAR P+REALV  HQ  RYT+ QL     + A AL+ 
Sbjct: 5   SYTQGTQDKPLLTQCIGDAFDATVARFPDREALVVHHQALRYTWRQLADAVDQHARALMA 64

Query: 76  MGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSM 135
           +G+ PGDR+GIW+ N AEW + Q A+A+VG +LVNINPAYR++E++YAL + GC+ ++  
Sbjct: 65  LGVQPGDRLGIWAPNCAEWCITQFASAKVGAILVNINPAYRSSELDYALGQSGCRWVICA 124

Query: 136 ARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTEL 195
             FKTSDY  ML+ L P     QPG L   + P+L+ VV +       +  PG L +  L
Sbjct: 125 DAFKTSDYHAMLQGLLPGLASSQPGALICERFPELRGVVSL-----ALSPPPGFLAWHAL 179

Query: 196 IARGNAADPR-LAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKL 254
            AR        LA   A L+  DPINIQ+TSGTTGFPKGATL+H NILNNG+ +GE + L
Sbjct: 180 QARAEVVSGEALAARQAQLRCDDPINIQYTSGTTGFPKGATLSHSNILNNGYMVGESLGL 239

Query: 255 TPADRLCIPVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVP 314
           T  DRL +PVPLYHCFGMV+ NL C THG+ ++YP+D FDPL  L+ V  E+ T L+GVP
Sbjct: 240 TEHDRLVVPVPLYHCFGMVMANLGCMTHGSALIYPSDAFDPLATLRAVAQEKATALYGVP 299

Query: 315 TMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVS 374
           TMFIAELDHP+  EF+LS+LRTGIMAG+ CP EVM+RV+ +M++ E+ IAYGMTETSPVS
Sbjct: 300 TMFIAELDHPQRGEFDLSSLRTGIMAGATCPIEVMRRVIGEMHMAEVQIAYGMTETSPVS 359

Query: 375 CQSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEA 434
            Q+     L +RV++VG+ QP LE K+VD + G  VP G+ GE CT+GYSVM GYW +  
Sbjct: 360 LQTGAADDLERRVTSVGRTQPRLESKVVDAE-GNTVPRGEIGELCTRGYSVMLGYWNNPK 418

Query: 435 KTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQD 494
            T E+ID  GWMHTGDLA MD +GYV IVGR KDM+IRGGENIYPRE+EEF + HP V D
Sbjct: 419 ATAESIDAEGWMHTGDLAVMDEQGYVRIVGRSKDMIIRGGENIYPRELEEFFFTHPAVAD 478

Query: 495 VQVVGVPDQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVT 554
           VQV+GVP  KYGEE+ AW+   PG   +E ++R + + +IAH+KVPRY RFV  FPMTVT
Sbjct: 479 VQVIGVPCSKYGEEIVAWVRLHPGHAVSEVELREWARARIAHFKVPRYFRFVDEFPMTVT 538

Query: 555 GKIQKFKIRDEMKDQL 570
           GK+QKF++R+   ++L
Sbjct: 539 GKVQKFRMREISVEEL 554


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: 884
Number of extensions: 32
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: 562
Length adjustment: 36
Effective length of query: 542
Effective length of database: 526
Effective search space:   285092
Effective search space used:   285092
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