GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Keio:15537
          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 (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