GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Klebsiella michiganensis M5al

Align Methylmalonate-semialdehyde dehydrogenase [inositol] (EC 1.2.1.27) (characterized)
to candidate BWI76_RS12820 BWI76_RS12820 NAD-dependent phenylacetaldehyde dehydrogenase

Query= reanno::Koxy:BWI76_RS03070
         (501 letters)



>FitnessBrowser__Koxy:BWI76_RS12820
          Length = 499

 Score =  248 bits (633), Expect = 4e-70
 Identities = 174/496 (35%), Positives = 255/496 (51%), Gaps = 32/496 (6%)

Query: 5   GNFIGGKTVTSGSNKTMPVFDPATGKVVREVTLSTAQEVSDAIQVARDAF--ESWSRTTP 62
           G ++ G    + S + + V++PATG+ +     + A +V  A+  A  AF   SW+  TP
Sbjct: 21  GLYLDGTQQAAESEQRLTVWNPATGQAIASTADANAADVDRAVMSAWRAFVSRSWAGRTP 80

Query: 63  LRRARVMFNFKMLLEQHAEELAGIIVSEHGKVFSDAMGELTRGMEV------VEFACGIP 116
             R R++  F  L+EQH EELA +   E GK  +     ++R  EV      + +  G+ 
Sbjct: 81  ADRERILLRFADLVEQHGEELAQLETLEQGKSIN-----ISRAFEVGCTLNWMRYTAGLT 135

Query: 117 HLIKGEFSSDV------GTGVDSYSLMQPLGVVAGITPFNFPAMVPMWMFPLALACGNSF 170
             I G  + DV      G    +++  +P+GVVAGI P+NFP M+ MW    ALA G S 
Sbjct: 136 TKISGR-TLDVSIPFPAGGRYQAWTKKEPVGVVAGIVPWNFPLMIGMWKVMPALAAGCSI 194

Query: 171 VLKPPALAPTAAVRLAELLKEAGLPDGVFNVVHCSNED-AEQLYRDPRIAAVSFVGSSGV 229
           V+KP    P   +R+AEL  EAG+PDGVFNVV  S       L   P +A VSF GS+  
Sbjct: 195 VIKPSETTPLTLLRVAELATEAGVPDGVFNVVTGSGAGCGAALTSHPLVAKVSFTGSTAT 254

Query: 230 AEHIYKTASAYGKRVQAFGAAKNHAIVMPDADLDATVNAIMGGAFGSAGERCMALPVVVA 289
            + I + A+    RV      KN AIV+ DAD    +  +M G+F + G+ C A   +  
Sbjct: 255 GKQIARVAADRLTRVTLELGGKNPAIVLKDADPQWVIEGLMTGSFLNQGQVCAASSRIY- 313

Query: 290 VGDETADKLIARLKPLVESLKVGPGCMRGKEENEMGPVVSDTHQKKVLGYIDKGVSEGAT 349
           +     D L++  +  V+SL+VGPG +   E +++ PVVS  H  KV  Y+D+   + A 
Sbjct: 314 IEAPLFDTLVSGFEQAVKSLQVGPGML---ESSQINPVVSQAHCAKVAAYLDEARQQKAE 370

Query: 350 LVVDGRKPQVPGFEEGYYVGGTLFDNVTPEMTIWREEIFGPVLGIVRVADYHSALELVNS 409
           L+     P      +GYY+  TL  N    + + REE+FGPV+ +VRVAD   AL L N 
Sbjct: 371 LISGHAGPDA----QGYYIAPTLVINPDAGLRLCREEVFGPVVNLVRVADGEEALLLAND 426

Query: 410 HEFGNGSAVFTSNGHTAREFVHDVQAGMVGVNVPVPVPMAFHSFGGWKRSVFGALNVHGP 469
            +FG  ++V+T +   A  +   +QAG V VN    +  A   FGG K+S  G     GP
Sbjct: 427 SDFGLTASVWTRDLTQALSYTDRLQAGTVWVNSHTLID-ANLPFGGMKQS--GTGRDFGP 483

Query: 470 DGVRFYTRMKTATVRW 485
           D +  +   K+  VR+
Sbjct: 484 DWLDDWCETKSVCVRY 499


Lambda     K      H
   0.319    0.135    0.404 

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: 601
Number of extensions: 28
Number of successful extensions: 7
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: 501
Length of database: 499
Length adjustment: 34
Effective length of query: 467
Effective length of database: 465
Effective search space:   217155
Effective search space used:   217155
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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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