Alignments for a candidate for aacS in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for aacS in Pseudomonas fluorescens FW300-N2E3

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate AO353_20355 AO353_20355 AMP-binding protein

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



>FitnessBrowser__pseudo3_N2E3:AO353_20355
          Length = 565

 Score =  627 bits (1617), Expect = 0.0
 Identities = 314/563 (55%), Positives = 401/563 (71%), Gaps = 7/563 (1%)

Query: 9   NSAPLVDSHARGATDVPLIEQTIGAFFADMVARQPEREALVSVHQGRRYTYAQLQTEAHR 68
           +SAP   S++RG+ D  L+  TIG  F + VA+ P+ +ALV  HQ  RY++AQL      
Sbjct: 4   HSAPPQHSYSRGSQDKALLAMTIGQAFDNTVAKYPQGDALVVRHQQLRYSWAQLAEAVDL 63

Query: 69  LASALLGMGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTAEVEYALNKVG 128
            A ALL +GL  GDR+GIW+ N A+W + Q A+A++G++LVNINPAYR++E+EY L + G
Sbjct: 64  HARALLALGLQTGDRLGIWAPNCAQWCISQFASAKIGVILVNINPAYRSSELEYVLKQSG 123

Query: 129 CKLLVSMARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWIDDEAGQGADEPG 188
           C+ LV    FKTSDY  ML+ LAPE   Q  GHL + +LP L+ V+ +D +   G     
Sbjct: 124 CQWLVCAGSFKTSDYHAMLQGLAPELAEQSIGHLHSERLPDLRGVISLDAQPPSG----- 178

Query: 189 LLRFTELIARGNAAD-PRLAQVAAGLQATDPINIQFTSGTTGFPKGATLTHRNILNNGFF 247
            L +++L   G      +L      L     +NIQ+TSGTTGFPKGATL+H NILNNG+ 
Sbjct: 179 FLPWSQLADLGAGVPVEQLKARQNSLHFDQAVNIQYTSGTTGFPKGATLSHYNILNNGYM 238

Query: 248 IGECMKLTPADRLCIPVPLYHCFGMVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERC 307
           +GE + LT  DRL IPVPLYHCFGMV+GNL C THG+T++YPND FDPL  L TV  E+ 
Sbjct: 239 VGESLGLTANDRLVIPVPLYHCFGMVMGNLGCVTHGSTMIYPNDAFDPLLTLTTVAQEKA 298

Query: 308 TGLHGVPTMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGM 367
           T L+GVPTMFIA LD PR AE +LSTLRTGIMAG+ CP EVM+RV+ +M++ E+ IAYGM
Sbjct: 299 TALYGVPTMFIAMLDQPRRAELDLSTLRTGIMAGATCPIEVMRRVISEMHMSEVQIAYGM 358

Query: 368 TETSPVSCQSSTDTPLSKRVSTVGQVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMH 427
           TETSPVS Q+     L  RV+TVG+ QP LE KI+D + G +VP G  GE CT+GYSVM 
Sbjct: 359 TETSPVSLQTGPSDDLELRVTTVGRTQPQLESKIID-EAGNLVPRGTIGELCTRGYSVML 417

Query: 428 GYWGDEAKTREAIDEGGWMHTGDLATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLY 487
           GYW +   T EAID+ GWMHTGDLATM+ EGYV I GR KDM+IRGGENIYPRE+EEF +
Sbjct: 418 GYWNNPQGTAEAIDQAGWMHTGDLATMNEEGYVCIAGRNKDMIIRGGENIYPRELEEFFF 477

Query: 488 RHPQVQDVQVVGVPDQKYGEELCAWIIAKPGTQPTEDDIRAFCKGQIAHYKVPRYIRFVT 547
            HP V DVQ+VG+P +KYGEE+ AWI   PG   +E +++A+CK +IAH+K PRY +FV 
Sbjct: 478 THPAVADVQIVGIPCEKYGEEIVAWIKFHPGHSVSEQELQAWCKERIAHFKTPRYFKFVE 537

Query: 548 SFPMTVTGKIQKFKIRDEMKDQL 570
            FPMTVTGKIQKF++R+   ++L
Sbjct: 538 EFPMTVTGKIQKFRMREISIEEL 560


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: 876
Number of extensions: 34
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: 565
Length adjustment: 36
Effective length of query: 542
Effective length of database: 529
Effective search space:   286718
Effective search space used:   286718
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)
SQLite3 databases

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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
the source code
instructions for running GapMind on your computer

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