GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aacS in Shewanella oneidensis MR-1

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate 202759 SO3664 long-chain-fatty-acid--CoA ligase (NCBI ptt file)

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



>lcl|FitnessBrowser__MR1:202759 SO3664 long-chain-fatty-acid--CoA
           ligase (NCBI ptt file)
          Length = 532

 Score =  218 bits (556), Expect = 4e-61
 Identities = 157/521 (30%), Positives = 253/521 (48%), Gaps = 36/521 (6%)

Query: 54  GRRYTYAQLQTEAHRLASALLG-MGLTPGDRVGIWSHNNAEWVLMQLATAQVGLVLVNIN 112
           G+  ++ +++ ++   A+ L     L PGDR+ I   N  ++V+      + GL+LVN N
Sbjct: 38  GKNSSFNEIERDSRYFAAYLQNNTNLKPGDRIAIQLPNITQFVIAAYGALRAGLILVNTN 97

Query: 113 PAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQPGHLQAAKL--PQL 170
           P Y   E+ +  N  G K LV +     SD L  L ++      +         L  PQ+
Sbjct: 98  PLYTERELIHQFNDSGAKALVVL-----SDLLPTLAKVVATTPIELVISTHPLDLIDPQV 152

Query: 171 KTVVWIDD-EAGQGADEPGLLRFTELIARGNAADPRLAQVAAGLQATDPINIQFTSGTTG 229
           +    + + E      +  LL FT  +       P L+ +AA         +Q+T GTTG
Sbjct: 153 QPKTGLKNVEFCHVLQQGALLPFTRFV-------PTLSDLAA---------LQYTGGTTG 196

Query: 230 FPKGATLTHRNILNNGFFIGECMKLTPA---DRLCIPVPLYHCFGMVLGNLACFTHGATI 286
             KGA LTH N+L N   +   +    +   D    P+P+YH +  ++  +  F  G   
Sbjct: 197 LSKGAMLTHGNMLANAAQVKSRIGSVISEGEDIFVAPLPIYHIYAFMVNLVLYFECGGCS 256

Query: 287 VYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAEFNLSTLRTGIMAGSPCPT 346
           V   +  D   +++T+     TG  G+ T+F+A    P F   N S L+  I  G+   T
Sbjct: 257 VLIPNPRDINGLIKTLAKYPFTGFAGLNTLFVALCHQPEFKALNFSHLKITISGGTAL-T 315

Query: 347 EVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLSKRVSTVGQVQPHLEVKIVDPDT 406
                + +Q     I+  YG++ETSPV    S + P  +++ T+G+     EVK++D ++
Sbjct: 316 AAAANLWQQTTGNTISEGYGLSETSPVI---SLNAPGYQKIGTIGKPVLGTEVKLLD-ES 371

Query: 407 GAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGDLATMDAEGYVNIVGRI 466
           G  V  G  GE   +G  VM GYW +  +T   +   G+  TGD+A ++ EG+  IV R 
Sbjct: 372 GNEVTQGTAGELAARGPQVMLGYWNNPQETANVMTPDGFFKTGDIAILNEEGFHQIVDRK 431

Query: 467 KDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEELCAWIIAKPGTQPTE--- 523
           KDM+I  G N+YP E+E  L  HP + +  VVGV D   GE + A+I+ K  +Q  E   
Sbjct: 432 KDMIIVSGFNVYPNEVENVLASHPNIIECAVVGVKDDHSGEAVKAFIVLKDDSQDHEKIK 491

Query: 524 DDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRD 564
             I  FC+ Q+  YK+P+ I F++  P +  GKI + ++++
Sbjct: 492 TAILNFCREQLTAYKLPKQIEFMSQLPKSTVGKILRRELKN 532


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: 702
Number of extensions: 37
Number of successful extensions: 6
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: 532
Length adjustment: 36
Effective length of query: 542
Effective length of database: 496
Effective search space:   268832
Effective search space used:   268832
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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