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_575 Long-chain-fatty-acid--CoA ligase (EC 6.2.1.3)

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



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_575
          Length = 505

 Score =  207 bits (526), Expect = 1e-57
 Identities = 144/475 (30%), Positives = 224/475 (47%), Gaps = 36/475 (7%)

Query: 52  HQGRRYTYAQLQTEAHRLASALLG-MGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVN 110
           + G   TYA+L+  +   A  L     L PGDR+ +   N   + +      + GL++VN
Sbjct: 45  NMGVTLTYAELERYSAAFAGYLQAHTDLMPGDRIAVQMPNVLHYPIAVFGALRAGLIVVN 104

Query: 111 INPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQL 170
            NP Y   E+ +     G + LV +  F        ++E+ P+   Q   +L  AK+  L
Sbjct: 105 TNPLYTAREMRHQFKDSGARALVYLNVFGQK-----VQEVLPDTDIQ---YLIEAKMGDL 156

Query: 171 KTVV--WIDDEAGQGADE-------PGLLRFTELIARGNAADPRLAQVAAGLQATDPINI 221
                 W+ +       +       P  + F   +  G     +   V  GL   D   +
Sbjct: 157 MPTAKGWLVNTLVSKVKKMVPDYSLPQAISFKSALRLGRGLGIKPLNV--GLD--DIAVL 212

Query: 222 QFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADR----------LCIPVPLYHCFG 271
           Q+T GTTG  KGA LTH N++ N      C+    AD           +  P+PLYH + 
Sbjct: 213 QYTGGTTGLAKGAMLTHGNLVANMQQARACLGQFGADGQPLLREGLEVMIAPLPLYHIYA 272

Query: 272 MVLGNLACFTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAEFNL 331
                +     G   V   +  D    ++ +++ R + L G+ T+F+A +DHP F   + 
Sbjct: 273 FTANCMCMMVTGNHNVLITNPRDIGNFIKELKNWRFSALLGLNTLFVALMDHPDFKTLDF 332

Query: 332 STLRTGIMAGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSKRVSTVG 391
           S+L+     G+       +R  EQ+    IT  YG+TETSPV+C +        R+ TVG
Sbjct: 333 SSLKLTNSGGTALVKATAERW-EQLTGCRITEGYGLTETSPVACTNPYGD--KSRIGTVG 389

Query: 392 QVQPHLEVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGDL 451
              P   +K+++ D G    +G+RGE C KG  +M GYW     T + +D  GW  +GD+
Sbjct: 390 LPVPGTALKVIN-DEGVEQSLGERGELCIKGPQIMKGYWQKPEATADVLDADGWFKSGDI 448

Query: 452 ATMDAEGYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYG 506
           A +D +G+V IV R KDM+I  G N+YP EIE+ +  HP+V +  V+GVPD++ G
Sbjct: 449 AVIDPDGFVRIVDRKKDMIIVSGFNVYPNEIEDVVMAHPKVANCAVIGVPDERSG 503


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: 703
Number of extensions: 37
Number of successful extensions: 5
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: 505
Length adjustment: 35
Effective length of query: 543
Effective length of database: 470
Effective search space:   255210
Effective search space used:   255210
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: 52 (24.6 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