Aligments for a candidate for aacS in Sinorhizobium meliloti 1021

GapMind for catabolism of small carbon sources

Aligments for a candidate for aacS in Sinorhizobium meliloti 1021

Align Acetoacetate--CoA ligase (EC 6.2.1.16) (characterized)
to candidate SMa0150 SMa0150 malonyl-CoA synthase

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



>FitnessBrowser__Smeli:SMa0150
          Length = 508

 Score =  230 bits (587), Expect = 9e-65
 Identities = 167/527 (31%), Positives = 256/527 (48%), Gaps = 45/527 (8%)

Query: 40  ARQPEREALVSVHQGRRYTYAQLQTEAHRLASALLGMGLTPGDRVGIWSHNNAEWVLMQL 99
           A +P+  A +    GR +TY  +   + R+AS L  +G+ PGDRV +    + E +++ L
Sbjct: 12  AARPD-SAFILTADGRVWTYGDMLEHSGRIASVLDALGVRPGDRVAVQVEKSPEALMLYL 70

Query: 100 ATAQVGLVLVNINPAYRTAEVEYALNKVGCKLLVSMARFKTSDYLGMLRELAPEWQGQQP 159
           A  + G V + +N AY  AE++Y       +L+V     K     G+ +  A        
Sbjct: 71  ACLRTGAVYLPLNTAYTLAELDYFFGDAEPRLIVCAPGAKE----GIAKHAAD------- 119

Query: 160 GHLQAAKLPQLKTVVWIDDEAGQGADEPGLLRFTELIARGNAADPRLAQVAAGLQATDPI 219
                A++  L       DE G G+    L+     +ARG A D       A     D  
Sbjct: 120 ---CGAEVETL-------DEKGGGS----LID----LARGKAPD----FPDADRGPDDLA 157

Query: 220 NIQFTSGTTGFPKGATLTHRNILNNGFFIGECMKLTPADRLCIPVPLYHCFGMVLGNLAC 279
            I +TSGTTG  KGA LTH N+L+N   + E  + T  DRL   +P++H  G+ + +   
Sbjct: 158 AILYTSGTTGRSKGAMLTHDNLLSNATTLREYWRFTADDRLIHALPIFHTHGLFVASNVI 217

Query: 280 FTHGATIVYPNDGFDPLTVLQTVQDERCTGLHGVPTMFIAELDHPRFAEFNLSTLRTGIM 339
              GA++ +    FD   VL+ +     T + GVPT ++  + +P       + +R  + 
Sbjct: 218 LLAGASMFFLPK-FDANEVLRLMPQS--TSMMGVPTFYVRLVQNPGLTHEATAGMRLFVS 274

Query: 340 AGSPCPTEVMKRVVEQMNLREITIAYGMTETSPVSCQSSTDTPLS--KRVSTVGQVQPHL 397
             +P   E   R   QM    I   YGMTET+      +T  P    +   TVG   P +
Sbjct: 275 GSAPLLAET-HRTFAQMTGHAILERYGMTETN-----MNTSNPYDGERIAGTVGFPLPGV 328

Query: 398 EVKIVDPDTGAVVPIGQRGEFCTKGYSVMHGYWGDEAKTREAIDEGGWMHTGDLATMDAE 457
            +++ DP++G  +P G+ G    KG +V  GYW    KT+      G+  TGDL  +D  
Sbjct: 329 SLRVADPESGRPLPKGETGMIEVKGPNVFKGYWRMPEKTQGEFRADGFFITGDLGRIDER 388

Query: 458 GYVNIVGRIKDMVIRGGENIYPREIEEFLYRHPQVQDVQVVGVPDQKYGEELCAWIIAKP 517
           GYV+IVGR KD+VI GG NIYP+E+E  + + P V +  V+G+P   +GE + A ++ KP
Sbjct: 389 GYVHIVGRGKDLVISGGYNIYPKEVETEIDQMPGVVETAVIGLPHPDFGEGVTAVVVRKP 448

Query: 518 GTQPTEDDIRAFCKGQIAHYKVPRYIRFVTSFPMTVTGKIQKFKIRD 564
           G    E  I    +G++A YK P+ + FV   P    GK+QK  +R+
Sbjct: 449 GAAIDERAILDGLEGRLARYKQPKRVIFVDDLPRNTMGKVQKNVLRE 495


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: 678
Number of extensions: 34
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 578
Length of database: 508
Length adjustment: 35
Effective length of query: 543
Effective length of database: 473
Effective search space:   256839
Effective search space used:   256839
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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Protein sequences (fasta format)
Organisms (tab-delimited)
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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, 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

GapMind for catabolism of small carbon sources