GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacF 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)



>NCBI__GCF_000009985.1:WP_011383248.1
          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:

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