GapMind for catabolism of small carbon sources

 

Aligments for a candidate for iolA in Escherichia coli BW25113

Align Methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial; MMSDH; Malonate-semialdehyde dehydrogenase [acylating]; Aldehyde dehydrogenase family 6 member A1; EC 1.2.1.18; EC 1.2.1.27 (characterized)
to candidate 15537 b1415 aldehyde dehydrogenase A, NAD-linked (NCBI)

Query= SwissProt::Q02253
         (535 letters)



>lcl|FitnessBrowser__Keio:15537 b1415 aldehyde dehydrogenase A,
           NAD-linked (NCBI)
          Length = 479

 Score =  216 bits (551), Expect = 1e-60
 Identities = 146/477 (30%), Positives = 235/477 (49%), Gaps = 10/477 (2%)

Query: 42  LFIDGKFVESKSDKWIDIHNPATNEVVGRVPQSTKAEMEAAVAACKRAFPAWADTSILSR 101
           ++IDG+FV  + D WID+ NPAT  V+ R+P     +   A+ A +RA P W     + R
Sbjct: 9   MYIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIER 68

Query: 102 QQVLLRYQQLIKENLKEIARLITLEQGKTLADAEGDVFRGLQVVEHACSVTSLMLGETMP 161
              L +    I+E   EI+ LI  E GK    AE +V      +++         GE + 
Sbjct: 69  ASWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQ 128

Query: 162 SITKDMDLYSYRLPLGVCAGIAPFNFPAMIPLWMFPMAMVCGNTFLMKPSERVPGATMLL 221
           S     ++  ++  LGV  GI P+NFP  +       A++ GNT ++KPSE  P   +  
Sbjct: 129 SDRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAF 188

Query: 222 AKLLQDSGAPDGTLNIIHGQHEAV-NFICDHPDIKAISFVGSNQAGEYIFERGSRNGKRV 280
           AK++ + G P G  N++ G+ E V   +  +P +  +S  GS  AGE I    ++N  +V
Sbjct: 189 AKIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKV 248

Query: 281 QANMGAKNHGVVMPDANKENTLNQLVGAAFGAAGQRC-MALSTAVLVGEAKKWLPELVER 339
              +G K   +VM DA+ E  +  +V +    +GQ C  A    V  G   +++  L E 
Sbjct: 249 CLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEA 308

Query: 340 AKNLRV-NAGDQPGADLGPLITPQAKERVCNLIDSGAKEGASILLDGRKIKVKGYENGNF 398
            + ++  N  ++    +GPLI   A ERV   +    +EGA +   G+ ++ KGY    +
Sbjct: 309 MQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGY----Y 364

Query: 399 VGPTIISNVKPSMTCYKEEIFGPVLVVLETETLDEAIKIVNDNPYGNGTAIFTTNGAIAR 458
             PT++ +V+  M+   EE FGPVL V+  +TL++AI + ND+ YG  ++I+T N  +A 
Sbjct: 365 YPPTLLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAM 424

Query: 459 KYAHMVDVGQVGVNVPIPVPLPMFSFTGSRSSFRGDTNFYGKQGIQFYTQLKTITSQ 515
           K    +  G+  +N      +  F   G R S  G  +  GK G+  Y Q + +  Q
Sbjct: 425 KAIKGLKFGETYINRENFEAMQGF-HAGWRKSGIGGAD--GKHGLHEYLQTQVVYLQ 478


Lambda     K      H
   0.318    0.133    0.389 

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: 530
Number of extensions: 25
Number of successful extensions: 4
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: 535
Length of database: 479
Length adjustment: 34
Effective length of query: 501
Effective length of database: 445
Effective search space:   222945
Effective search space used:   222945
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint 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