GapMind for catabolism of small carbon sources

 

Alignments for a candidate for DVU3033 in Shewanella amazonensis SB2B

Align Iron-sulfur cluster-binding protein (characterized, see rationale)
to candidate 6938323 Sama_2442 iron-sulfur cluster-binding protein (RefSeq)

Query= uniprot:Q726S3
         (717 letters)



>FitnessBrowser__SB2B:6938323
          Length = 466

 Score =  254 bits (648), Expect = 9e-72
 Identities = 155/418 (37%), Positives = 219/418 (52%), Gaps = 24/418 (5%)

Query: 35  RASRANAFKDIDE-KAIIAEVADAKDHAAKNMDTLYAQFKAEAEKRGVKVHLARTAAEAN 93
           R  R  A   + E + + A  +  K H    +      F+A+   +GVKVH A+  AE N
Sbjct: 33  REKRDRAASSLPEWETLRALGSQIKLHTLNQLPGYLEAFEAKCLSQGVKVHWAKDGAEHN 92

Query: 94  EIIARIARDNNCKKAIKSKSMTAEETHLNHRLEEDNVEVIETDLGEWIIQMRHEGPSHMV 153
            I+  I   +  KK +KSKSM  EE HLN  LE   +EVI+TDLGE IIQ+ H+ PSH+V
Sbjct: 93  RIVHDILSRHGVKKLVKSKSMLTEECHLNPFLEGKGIEVIDTDLGERIIQLNHQPPSHIV 152

Query: 154 MPAIHLSRYQVADLFSE-VTKQKQEVDIQRLVKVARRELRTHFATADMGISGANFAVAET 212
           +PAIH+ + +V DLF E +   K E D  RL + AR  LR  F +AD  ++G N AVA  
Sbjct: 153 VPAIHMKKEEVGDLFHEKLGTPKGESDPTRLTRAARAHLREQFLSADAAMTGVNMAVASE 212

Query: 213 GTIGLVTNEGNARLVTTLPRVHVALAGLDKLVPTLHDALRSLKVLPRNATGQAITSYVTW 272
           G + + TNEGNA +   LP++ +   G+DK+VP L  A   L++L RNATGQ IT+Y   
Sbjct: 213 GAVIVCTNEGNADMGANLPKLQLHSMGIDKIVPDLDSAAVLLRMLARNATGQPITTY--- 269

Query: 273 IGGANECEACVDGRKEMHIVFLDNGRRALAEDPLFSQVLRCVRCGACANVCPVYRLVGGH 332
               +          EMH++ +DNGR A+  D L  + L+C+RCG C N CPVYR  GG+
Sbjct: 270 ----SSLYRTPKPGGEMHVIIVDNGRSAMMRDKLLGEALKCIRCGGCLNTCPVYRRSGGY 325

Query: 333 KMGHIYIGAIGLILTYFFHGRDKARNLVQNCINCESCKHICAGGIDLPRLIKEIRARLNE 392
             GH   G IG+ +       D   +    C  C SC  +C   + L ++I   R    E
Sbjct: 326 SYGHTIPGPIGIAVG---ADEDDTHSSPWACTLCGSCSFVCPTKVPLDKIIFHRRRLYAE 382

Query: 393 EEGMPVETT----LMGKMLKNRKLFHTLLRFAKWA--------QKPVTGGTPYIRHLP 438
            + +P   +    L+G+ + +  L  T +  A+ A         KP++G     R LP
Sbjct: 383 RKSLPYGKSGYMPLVGRFMASPLLLDTGMAAARIALKILPHSLLKPMSGAWGKYRELP 440


Lambda     K      H
   0.321    0.135    0.402 

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: 755
Number of extensions: 36
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: 717
Length of database: 466
Length adjustment: 36
Effective length of query: 681
Effective length of database: 430
Effective search space:   292830
Effective search space used:   292830
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 (21.9 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