GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gabD in Magnetospirillum magneticum AMB-1

Align Succinate-semialdehyde dehydrogenase, mitochondrial; At-SSADH1; Aldehyde dehydrogenase family 5 member F1; NAD(+)-dependent succinic semialdehyde dehydrogenase; Protein ENLARGED FIL EXPRESSING DOMAIN 1; EC 1.2.1.24 (characterized)
to candidate WP_011383248.1 AMB_RS04115 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase

Query= SwissProt::Q9SAK4
         (528 letters)



>lcl|NCBI__GCF_000009985.1:WP_011383248.1 AMB_RS04115
           5-carboxymethyl-2-hydroxymuconate semialdehyde
           dehydrogenase
          Length = 485

 Score =  349 bits (896), Expect = e-100
 Identities = 194/483 (40%), Positives = 291/483 (60%), Gaps = 18/483 (3%)

Query: 56  LIGGKWLDSYDNKTIKVNNPATGEIIADVACMGTKETNDAIASSYEAFTSWSRLTAGERS 115
           LI G+ ++S    TI   NPA  E+I  +A  G  E   A+A++ EAF  W+ L A +R+
Sbjct: 5   LINGRQVESAS--TIANLNPANNEVICQIAAGGEAEVAQAVAAAKEAFPKWAGLPASQRA 62

Query: 116 KVLRRWYDLLIAHKEELGQLITLEQGKPL---KEAIGEVAYGASFIEYYAEEAKRVYGDI 172
           K+LR+  DL+  H +E+ +L +L+ G+     K+ +  V   A    ++A+    V G+ 
Sbjct: 63  KLLRKVGDLINQHVDEIAKLESLDTGQSYWRTKKML--VPRAADNFYFFADTCCHVDGET 120

Query: 173 IPPNLSDRRLLVLKQPVGVVGAITPWNFPLAMITRKVGPALASGCTVVVKPSELTPLTAL 232
            P N  D     L QPVGVVG I+PWN P    T K  P LA G T V+K SEL+PL+A 
Sbjct: 121 YPTN--DHLNYTLYQPVGVVGLISPWNVPFMTATWKTAPCLAFGNTAVLKMSELSPLSAD 178

Query: 233 AAAELALQAGVPPGALNVVMGNAPEIGDALLTSPQVRKITFTGSTAVGKKLMAAAAPTVK 292
              +L L+AG+P G  N+V G    +G+AL+  P VR ++FTGSTA G +++ +    +K
Sbjct: 179 RLGQLILEAGIPAGVFNIVHGYGSAVGEALVKHPDVRGVSFTGSTATGNRIIQSGG--LK 236

Query: 293 KVSLELGGNAPSIVFDDADLDVAVKGTLAAKFRNSGQTCVCANRVLVQDGIYDKFAEAFS 352
           K S+ELGG +P+I+FDD D + AV   + A + N+G++C    R+LVQDG+YD+F  A +
Sbjct: 237 KYSMELGGKSPNIIFDDCDFERAVDAAIVAVYGNNGESCTNGTRILVQDGLYDRFVAALA 296

Query: 353 EAVQKLEVGDGFRDGTTQGPLINDAAVQKVETFVQDAVSKGAKIIIGGKRHSLGMT---- 408
           E  +K+ VGD   + T  GP+I     +KV ++++  +S+GA+++ GG     G+     
Sbjct: 297 ERTRKVVVGDPLDEATNVGPMITRDHWKKVTSYIELGISEGARVVAGGLGTPEGLAPHLK 356

Query: 409 ---FYEPTVIRDVSDNMIMSKEEIFGPVAPLIRFKTEEDAIRIANDTIAGLAAYIFTNSV 465
              F  PTV+ DV ++  +++EEIFGPVA +IRFK E +A++IAN T  GLA+Y++T + 
Sbjct: 357 NGNFVRPTVLADVDNSWRVAQEEIFGPVACVIRFKDEAEALKIANATSYGLASYVWTENG 416

Query: 466 QRSWRVFEALEYGLVGVNEGLISTEVAPFGGVKQSGLGREGSKYGMDEYLEIKYVCLGDM 525
            R+ R+ E +E GLV VN   +     PFGG+K SG GREG  Y  + +LE+K VC+   
Sbjct: 417 ARAIRMAEGIEAGLVFVNSQNVRDLRQPFGGIKGSGTGREGGHYSYEAFLEVKNVCVSKG 476

Query: 526 NRH 528
           + H
Sbjct: 477 SHH 479


Lambda     K      H
   0.317    0.134    0.383 

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: 618
Number of extensions: 31
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: 528
Length of database: 485
Length adjustment: 34
Effective length of query: 494
Effective length of database: 451
Effective search space:   222794
Effective search space used:   222794
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 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