GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Dyella japonica UNC79MFTsu3.2

Align Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27) (characterized)
to candidate N515DRAFT_3729 N515DRAFT_3729 aminomuconate-semialdehyde/2-hydroxymuconate-6-semialdehyde dehydrogenase

Query= reanno::pseudo1_N1B4:Pf1N1B4_1229
         (505 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3729
          Length = 483

 Score =  246 bits (628), Expect = 1e-69
 Identities = 166/482 (34%), Positives = 251/482 (52%), Gaps = 15/482 (3%)

Query: 15  LIDGEWVESQTTEWHDIVNPATQQVLAKVPFATAAEVDAAISAAHRAFQTWKLTPIGARM 74
           LIDG     +   W ++  PAT +V A  P ++ A+VDAA++AA  A   W  TP   R 
Sbjct: 9   LIDGRLQAPRQERWLEVFEPATGEVFAHCPESSFADVDAAVAAAVAAAPGWAATPSEQRA 68

Query: 75  RIMLKLQALIREHSKRIAVVLSNEQGKTIADAEG-DIFRGLEVVEH-ACSIGSLQMGEFA 132
           R++ +L  LI       A + S + GK ++ A   DI R +  + + A +I        A
Sbjct: 69  RLLQRLADLIEARLDEFAALESRDSGKPLSLARSLDIPRAVSNLRYFAAAIVPWSSESHA 128

Query: 133 ENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTFVLKPSEQDPMSTML 192
             +  G   YTLRQP+GV A I+P+N P  +  W    A+A GN  V KPSE  P +  L
Sbjct: 129 MEL--GAINYTLRQPLGVVACISPWNLPLYLFTWKIAPALAAGNAVVAKPSEITPCTAAL 186

Query: 193 LVELAIEAGIPPGVLNVVHG-GKDVVDALCTHKDIKAVSFVGSTAVGTHVYDLAGKHGKR 251
           L EL+IEAG PPGVLN+V G G +V  AL  H+D+KAVSF GST  G  +   A    K+
Sbjct: 187 LGELSIEAGFPPGVLNIVQGRGPEVGQALVEHRDVKAVSFTGSTRTGAQIAAAAAPRFKK 246

Query: 252 VQSMMGAKNHAVVLPDANREQA-LNALVGAGFGAAGQRCMATS-VVVLVGAAKQWLPDLK 309
           +   +G KN A+V  DA+   A L+ +V +GF   G+ C+  S ++V       +     
Sbjct: 247 LSLELGGKNPAIVFADADLSDANLDTIVRSGFANQGEICLCGSRLLVQRSIYDAFRERYL 306

Query: 310 ALAQKLKVNAGSEPGTDVGPVISKRAKARILDLIESGIKEGAKLELDGRDISVPGYEKGN 369
           A  + L+V    E  TD+G ++S+    ++   I     EG ++   G  +++PG   G 
Sbjct: 307 AKVRALRVGDPREAATDLGALVSREHFDKVTGCIAQARAEGGRVLCGGDALALPGPLAGG 366

Query: 370 -FVGPTLFSGVTPEMQIYTQEIFGPVLVVLEVDTLDQAIALVNANPFGNGTGLFTQSGAA 428
            +V PT+  G+ PE     QEIFGPV+ ++  D   QA+A+ N   +G    L+T   + 
Sbjct: 367 WYVAPTVIEGLGPETATNQQEIFGPVVTLIPFDDEAQALAIANGTGYGLAASLWTTDLSR 426

Query: 429 ARKFQTEIDVGQVGINIPI--PVPVPFFSFTGSRGSKLGDLGPYGKQVVQFYTQTKTVTA 486
           A +F  ++D G V IN  +   +  P   F G++ S +G  G  G + ++F+T+ K +  
Sbjct: 427 AHRFGAQLDFGIVWINCWLLRDLRTP---FGGAKQSGVGREG--GVEALRFFTEPKNICI 481

Query: 487 RW 488
           R+
Sbjct: 482 RY 483


Lambda     K      H
   0.319    0.135    0.397 

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: 566
Number of extensions: 30
Number of successful extensions: 5
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: 505
Length of database: 483
Length adjustment: 34
Effective length of query: 471
Effective length of database: 449
Effective search space:   211479
Effective search space used:   211479
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: 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