GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Shewanella sp. ANA-3

Align isobutanoate/2-methylbutanoate--CoA ligase (EC 6.2.1.1) (characterized)
to candidate 7025315 Shewana3_2475 AMP-binding domain protein (RefSeq)

Query= metacyc::MONOMER-20125
         (556 letters)



>FitnessBrowser__ANA3:7025315
          Length = 574

 Score =  163 bits (412), Expect = 2e-44
 Identities = 156/565 (27%), Positives = 254/565 (44%), Gaps = 81/565 (14%)

Query: 19  FLERAATVYGDCTSVVYDAVSYTWSQTHRRCLC----LASSIASLGIENGHVVSVLAPNV 74
           +L   A VY +  +VV +     W+  +R+ L     LA+ +  LGI  G  V + +PN 
Sbjct: 37  YLNDIANVYPEQLAVVVNHQDIRWN--YRQYLAQIDALATGLLKLGIGPGDRVGIWSPNN 94

Query: 75  PQMYELHFAVPMAGAILNAVNLRLDARTISILLHH-------------SESKLIFVDHLS 121
            +     FA    GAI+  +N       +   L +             S + L  +  L+
Sbjct: 95  IEWCLTQFATAKIGAIMVCINPAYRPEELQYALTNVGCRAVICADKFKSSNYLQMLYELA 154

Query: 122 RDLILEAIALFPKQAPVPRLVFMADESESGNSSELGKEFFCSYKDLIDRGDPDFKWVMPK 181
            +L + A      +A +P L F+       +   L      ++ DL+     D K  + +
Sbjct: 155 PELKVCAAGQLQAKA-LPDLQFVIRMGAEQSPGML------NFDDLLVEVTADDKAALER 207

Query: 182 -----SEWDPMILNYTSGTTSSPKGVVHCHRGIF---IMTVDSLIDWGVPKQPVYLWTLP 233
                S +D + + +TSGTT SPKG    H  I     +  +++      K  +    +P
Sbjct: 208 IAESLSPYDAINIQFTSGTTGSPKGATLSHHNILNNGYLVAEAMKFTCEDKLCI---PVP 264

Query: 234 MFHANGWSYPWGMAAVGGTNICLRK----------FDSEIIYDMIKRHGVTHMCGAPVVL 283
           ++H  G         V G  +CL K          FD     ++++R   T + G P + 
Sbjct: 265 LYHCFGM--------VLGNLVCLAKGAAAVFPGDSFDPLTTLEVVERERCTALHGVPTMF 316

Query: 284 NMLSNAPGSE-----PLKTTVQIMTAGAPPPSAVLFRTESLGFA--VSHGYGLTETAGLV 336
                 P  +      L+T V    AGA  P  V+ R ++L +   V  GYG TE + L 
Sbjct: 317 IAELEHPEFKRFDLSSLRTGVM---AGATCPEEVMRRVQNLMYMQEVLIGYGQTECSPL- 372

Query: 337 VSCAWKKEWNHLPATERARLKSRQGVGTVM-QTKIDVVDPVTGAAVKRDGSTLGEVVLRG 395
                    NH+   +    K    VG  +  T++ +VD   G  +  +  T GEV  RG
Sbjct: 373 ---------NHITEIDSPVEKRVLTVGRALPHTEVKIVDEF-GEVLPIN--TPGEVCSRG 420

Query: 396 GSVMLGYLKDPEGTAKSMTADGWFYTGDVGVMHPDGYLEIKDRSKDVIISGGENLSSVEV 455
             +M  Y  DPE TA ++ ++GW ++GD+G M   GY++I  R KD+II GGEN+   E+
Sbjct: 421 YCIMQCYWNDPEKTAATIDSEGWLHSGDIGQMDEQGYVQIVGRIKDMIIRGGENIYPREI 480

Query: 456 ESILYSHPDILEAAVVARPDEFWGETPCAFVSLKKGLTKKPTEKEIVEYCRSKLPRYMVP 515
           E  LY+H D+ +AAV     + +GE  CA++ ++ G T   +E++I  +   K   + VP
Sbjct: 481 EEKLYTHKDVQDAAVFGVHSDKYGEEVCAWIKIRSGAT--ISEEDIRHFLTEKFAYFKVP 538

Query: 516 KTVVFKEELPKTSTGKVQKFILRDM 540
           + + F E+ P T TGK+QKF +R++
Sbjct: 539 RYIKFVEQYPMTVTGKIQKFKMREL 563


Lambda     K      H
   0.319    0.135    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: 725
Number of extensions: 36
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: 2
Length of query: 556
Length of database: 574
Length adjustment: 36
Effective length of query: 520
Effective length of database: 538
Effective search space:   279760
Effective search space used:   279760
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 (21.7 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