GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nbaE in Magnetospirillum magneticum AMB-1

Align 2-aminomuconate 6-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate WP_011385953.1 AMB_RS18195 DUF1487 domain-containing protein

Query= metacyc::MONOMER-13361
         (500 letters)



>NCBI__GCF_000009985.1:WP_011385953.1
          Length = 496

 Score =  282 bits (722), Expect = 2e-80
 Identities = 162/451 (35%), Positives = 251/451 (55%), Gaps = 10/451 (2%)

Query: 39  NPVNGKLISDVFEADAKQVNEAVVAAQNALKGPWGKLSVQDRAALIHKIADGIQARFEEF 98
           NP  G++I        + V+ AV++A+ A K  W K S + R  L+ +    + A  EE 
Sbjct: 39  NPATGEIIGTAAFGTKEDVDIAVISAKAAQKD-WAKQSARARGKLVAECGRVLSAHVEEL 97

Query: 99  VAAEVADTGRPVHQARTLDIPRAIANFRTFADLAKTSHTDLFEMSTSDGSGALNYTVRKP 158
                 +TG+ +     ++       F  F  L      +    +       L  TVR+P
Sbjct: 98  GRLVALETGKALRTESRVEAGVLADMFTFFGGLGSELKGETIPFNPD----MLTVTVREP 153

Query: 159 LGVIGVISPWNLPLLLFTWKVAPALACGNTVVAKPSEESPSSATLLAEVMHDAGVPPGVF 218
           +GV+G I PWN+PLLL   K A AL  GN+VV K +EE+P +   +AE+M+   +PPG+F
Sbjct: 154 VGVVGCIIPWNVPLLLMAMKAAAALVAGNSVVVKSAEEAPLTVLRVAEIMNTV-LPPGLF 212

Query: 219 NLIHGFGKDSAGEFLTQHPGISALTFTGESKTGSTIMKAVADGVKEVSFELGGKNAAVVF 278
           N++ GFG +  G  L +HP +  +TFTG  +TG  + KA A+ +  V+ ELGGK+  +V 
Sbjct: 213 NMLSGFGPE-CGAPLVEHPDVKKVTFTGSVETGRIVYKAAAEKLIPVTLELGGKSPMIVC 271

Query: 279 ADADLDAAIEGVLRSS-FTNSGQVCLCSERVYVHRSIFDEFVSGLKVEAERLVVGYPDQD 337
           ADAD+D A+ G L    FT  GQ C  S R++VH SI DEFV+ +K + + +V+G P  +
Sbjct: 272 ADADMDQAVAGALAGMRFTRQGQSCTASSRLFVHESIHDEFVAKVKAKVDAMVMGDPLDE 331

Query: 338 GVNMGPLISHGHRDKVLSYYRLAVD-EGATVVTGGGVPKFNDERDQGAYVQPTIWTGLSD 396
             ++G ++S G  ++V SY ++  + +GAT      +P  + +  +G +VQP I+TG+ +
Sbjct: 332 KTDIGTIVSDGQLERVRSYIKIGEETKGATKHVCSALPT-DPKLAKGRFVQPVIFTGMKN 390

Query: 397 KARCVTEEIFGPVCHISPFDDEDEVINRVNDSNYGLACAIWTTNLSRAHRVSRQIHVGLV 456
             R   EEIFGPVC +  + D ++V+ + NDS YGLA +IWT +   A   ++++  G V
Sbjct: 391 SDRLCQEEIFGPVCAVIKWSDYEDVLAQANDSEYGLAASIWTRDFKLAMDATKRLEAGFV 450

Query: 457 WVNTWYLRDLRTPFGGVKLSGLGREGGRFSM 487
            VN   +      +GGVK SG+G+E    SM
Sbjct: 451 QVNQNLVVQPGLSYGGVKTSGIGKEASLESM 481


Lambda     K      H
   0.318    0.135    0.405 

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: 528
Number of extensions: 25
Number of successful extensions: 7
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: 500
Length of database: 496
Length adjustment: 34
Effective length of query: 466
Effective length of database: 462
Effective search space:   215292
Effective search space used:   215292
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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