GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Phaeobacter inhibens BS107

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate GFF3354 PGA1_c34070 long-chain-fatty-acid- CoA ligase IcfB

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



>FitnessBrowser__Phaeo:GFF3354
          Length = 500

 Score =  209 bits (532), Expect = 2e-58
 Identities = 161/522 (30%), Positives = 241/522 (46%), Gaps = 78/522 (14%)

Query: 59  YAQLQTEAHRLASALLGMGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNINPAYRTA 118
           Y +L   A R+A+AL+  G+ PGDRV      +   + + L T   G + + +NPAY  A
Sbjct: 34  YGELFAGAERMAAALVSRGVAPGDRVAAQVDKSLAAIQLYLGTVMAGAIFLPLNPAYTEA 93

Query: 119 EVEYALNKVGCKLLV-SMARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQLKTVVWID 177
           EV Y +     ++ V +  R ++      LR +A E                  TV+ +D
Sbjct: 94  EVAYFIGDATPRVFVCNPVRHES------LRAVAGE-----------------ATVLTLD 130

Query: 178 DEAGQGADEPGLLRFTELIARGNAADPRLAQVAAGLQATDPIN--------IQFTSGTTG 229
            E GQG+                     LA +AAG    +PI         I +TSGTTG
Sbjct: 131 GE-GQGS---------------------LADLAAGHAGFEPIERKPSDLAAILYTSGTTG 168

Query: 230 FPKGATLTHRNILNNGFFIGECMKLTPADRLCIPVPLYHCFGMVLGNLACFTHGATIVYP 289
             KGA L+H N+ +N   + +  + T  D L   +P++H  G+ +        GA +V  
Sbjct: 169 RSKGAMLSHENLYSNSLTLRDYWQFTAEDVLIHALPIFHTHGLFVATNVALLAGAQVVL- 227

Query: 290 NDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAEFNLSTLRTGIMAGSPCPTEVM 349
             GFD   +L  + +   T L GVPT +   L   R      + +R  I   +P   E  
Sbjct: 228 LPGFDAEAILAAMPN--ATALMGVPTFYTRLLVDARLTPDLAANMRLFISGSAPLLVETH 285

Query: 350 KRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLS--KRVSTVGQVQPHLEVKIVDPDTG 407
           ++  E      I   YGMTET+      ST  P    +   TVG   P +E ++   +  
Sbjct: 286 EQ-WEARTGHRILERYGMTETN-----MSTSNPYDGVRVAGTVGPPLPGVEARVTLDN-- 337

Query: 408 AVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGDLATMDAEGYVNIVGRIK 467
           A +P+G+ G    +G +V  GYW    KT E +   GW  TGDLA +D+ GYV IVGR K
Sbjct: 338 AEIPLGEIGVLEVRGPNVFQGYWQMPEKTAEELRPDGWFITGDLAKIDSNGYVTIVGREK 397

Query: 468 DMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEELCAWIIAKPGTQPTED--- 524
           D+VI GG N+YP+E+E  +   P V +  V+GVP   +GE + A ++      PTE+   
Sbjct: 398 DLVISGGFNVYPKEVETLIDDLPGVLESAVIGVPHPDFGEAVVAVVV------PTEEGTD 451

Query: 525 --DIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRD 564
              I+A     +A +K P++I  +   P    GK+QK  +R+
Sbjct: 452 AASIQAALSEHLAKFKQPKHIALMDELPRNTMGKVQKKALRE 493


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: 615
Number of extensions: 24
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 578
Length of database: 500
Length adjustment: 35
Effective length of query: 543
Effective length of database: 465
Effective search space:   252495
Effective search space used:   252495
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