GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Paraburkholderia bryophila 376MFSha3.1

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate H281DRAFT_06226 H281DRAFT_06226 long-chain acyl-CoA synthetase

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



>FitnessBrowser__Burk376:H281DRAFT_06226
          Length = 557

 Score =  235 bits (600), Expect = 3e-66
 Identities = 171/524 (32%), Positives = 252/524 (48%), Gaps = 22/524 (4%)

Query: 51  VHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVN 110
           V  G+  +Y +L   + +LA+     GL  G RV I   N  ++ +   A  + G V+VN
Sbjct: 43  VCMGKEISYGELDALSRKLAAWFQSKGLARGARVAIMMPNVLQYPVAIAAILRAGYVVVN 102

Query: 111 INPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQPGHLQAAKLPQL 170
           +NP Y   E+E+ L   G + +V +  F  +    +             G L   K   +
Sbjct: 103 VNPLYTPRELEHQLKDSGAEAIVLLENFAVTLQAVVRNTAVKHIVVAAMGDLMGVKGAVV 162

Query: 171 KTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQVAAGLQATDPIN-IQFTSGTTG 229
             VV    +       PG ++F   IA G     +  Q     Q  D +  +Q+T GTTG
Sbjct: 163 NFVVRQVKKMVPAWSLPGHVKFNTAIAEGERQTFKPVQ-----QGPDDVAFLQYTGGTTG 217

Query: 230 FPKGATLTHRNILNNGFFIGECMKLTPADRL-------CIPVPLYHCFGM-VLGNLACFT 281
             KGATL HRN++ N       +     DR         + +PLYH F + V G L   T
Sbjct: 218 VAKGATLLHRNLIANVLQSEIWLNPVRTDRTDIEQFITVVALPLYHVFALTVCGLLTIRT 277

Query: 282 HGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAEFNLSTLRTGIMAG 341
            G  ++ PN    P  +++ +Q    T +  V T++ A L++P F + + S L      G
Sbjct: 278 GGLGVLIPNPRDIP-GMIKALQGYAITTIPAVNTLYNALLNNPDFHKLDFSKLIAANGGG 336

Query: 342 SPCPTEVMKRVVEQMNLREITIAYGMTETSP-VSCQSSTDTPLSKRVSTVGQVQPHLEVK 400
                 V KR  E  +   I   YG++ETSP V+C   T T  S    T+G   P  EV 
Sbjct: 337 MAVQEAVAKRWFENTHT-PIIEGYGLSETSPCVTCNPVTVTEYS---GTIGLPLPSTEVS 392

Query: 401 IVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGDLATMDAEGYV 460
           I D D G  VP+GQ GE C +G  VM GYW    +T + +   G+  +GD+  M+ +G+V
Sbjct: 393 IRD-DEGNEVPLGQPGEICIRGPQVMAGYWNRPDETAKVMTSDGFFRSGDVGFMNEQGFV 451

Query: 461 NIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEELCAWIIAKPGTQ 520
            IV R KDM++  G N+YP EIE+ + R P V +V  VGVPDQ  GE +  +++ K    
Sbjct: 452 KIVDRKKDMILVSGFNVYPNEIEDVVARLPGVFEVAAVGVPDQHSGEAVKLFVVRKDDAL 511

Query: 521 PTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRD 564
            T+ DI A+CK Q+  YK P+ + F T  P +  GKI + ++RD
Sbjct: 512 -TDADIFAYCKQQLTGYKRPKIVEFRTELPKSNVGKILRRELRD 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: 732
Number of extensions: 44
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: 557
Length adjustment: 36
Effective length of query: 542
Effective length of database: 521
Effective search space:   282382
Effective search space used:   282382
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