GapMind for catabolism of small carbon sources

 

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

Align 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate WP_011383248.1 AMB_RS04115 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase

Query= metacyc::MONOMER-20632
         (478 letters)



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

 Score =  314 bits (805), Expect = 4e-90
 Identities = 191/479 (39%), Positives = 268/479 (55%), Gaps = 22/479 (4%)

Query: 5   LRHYIGGERVAADAPAESLNPSNTNDVVAKVPMGGQAEVDAAVDAARKAFPAWADASPEV 64
           ++H I G +V + +   +LNP+N N+V+ ++  GG+AEV  AV AA++AFP WA      
Sbjct: 2   IKHLINGRQVESASTIANLNPAN-NEVICQIAAGGEAEVAQAVAAAKEAFPKWAGLPASQ 60

Query: 65  RSDLLDKVGSTIIARSADIGRLLAREEGKTLAEGIGETV-RAGRIFKYFAGEALRRHGQN 123
           R+ LL KVG  I     +I +L + + G++        V RA   F +FA       G+ 
Sbjct: 61  RAKLLRKVGDLINQHVDEIAKLESLDTGQSYWRTKKMLVPRAADNFYFFADTCCHVDGET 120

Query: 124 LESTRPGVEIQTYRQAVGVYGLITPWNFPIAIPAWKAAPALAFGNTVVIKPAGPTPATAN 183
              T   +    Y Q VGV GLI+PWN P     WK AP LAFGNT V+K +  +P +A+
Sbjct: 121 YP-TNDHLNYTLY-QPVGVVGLISPWNVPFMTATWKTAPCLAFGNTAVLKMSELSPLSAD 178

Query: 184 VLADIMAECGAPAGVFNMLFGRGS-MGDALIKHKDVDGVSFTGSQGVGAQVAAAAVARQA 242
            L  ++ E G PAGVFN++ G GS +G+AL+KH DV GVSFTGS   G ++  +   +  
Sbjct: 179 RLGQLILEAGIPAGVFNIVHGYGSAVGEALVKHPDVRGVSFTGSTATGNRIIQSGGLK-- 236

Query: 243 RVQLEMGGKNPLIVLDDADLERAVAIALDGSFFATGQRCTASSRLIVQDGIHDKFVALLA 302
           +  +E+GGK+P I+ DD D ERAV  A+   +   G+ CT  +R++VQDG++D+FVA LA
Sbjct: 237 KYSMELGGKSPNIIFDDCDFERAVDAAIVAVYGNNGESCTNGTRILVQDGLYDRFVAALA 296

Query: 303 EKVAALRVGDALDPNTQIGPAVSEDQMETSYRYIDIAASEGGRVVTGGDRIKLDNP---- 358
           E+   + VGD LD  T +GP ++ D  +    YI++  SEG RVV GG    L  P    
Sbjct: 297 ERTRKVVVGDPLDEATNVGPMITRDHWKKVTSYIELGISEGARVVAGG----LGTPEGLA 352

Query: 359 -----GWYVRPTLIADTQAGMRINNEEVFGPVASTIRVKSYEEALEIANGVEFGLSAGIA 413
                G +VRPT++AD     R+  EE+FGPVA  IR K   EAL+IAN   +GL++ + 
Sbjct: 353 PHLKNGNFVRPTVLADVDNSWRVAQEEIFGPVACVIRFKDEAEALKIANATSYGLASYVW 412

Query: 414 TTSLKHARHFQRYARAGMTMVNLATAGVDYHVPFGGTKSSSYGAREQGFAAVEFFTQTK 472
           T +   A        AG+  VN      D   PFGG K S  G RE G  + E F + K
Sbjct: 413 TENGARAIRMAEGIEAGLVFVNSQNVR-DLRQPFGGIKGSGTG-REGGHYSYEAFLEVK 469


Lambda     K      H
   0.317    0.133    0.384 

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: 583
Number of extensions: 22
Number of successful extensions: 6
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: 478
Length of database: 485
Length adjustment: 34
Effective length of query: 444
Effective length of database: 451
Effective search space:   200244
Effective search space used:   200244
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