GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dopDH in Mucilaginibacter mallensis MP1X4

Align α-ketoglutaric semialdehyde dehydrogenase subunit (EC 1.2.1.26) (characterized)
to candidate WP_091368988.1 BLU33_RS02870 aldehyde dehydrogenase (NADP(+))

Query= metacyc::G1G01-1343-MONOMER
         (525 letters)



>NCBI__GCF_900105165.1:WP_091368988.1
          Length = 527

 Score =  461 bits (1185), Expect = e-134
 Identities = 254/517 (49%), Positives = 324/517 (62%), Gaps = 2/517 (0%)

Query: 3   LTGNLLIGQRPVTGSRDAIRAIDPTTGQTLEPAYLGGTGEHVAQACALAWAAFDAYRETS 62
           + GN +I          A    DP+TG+ L   +       + +    A AAF  Y+ T 
Sbjct: 2   INGNNIIACNYTEIEGQAFTVADPSTGEKLSGEFYEADTLIIDKTLNAATAAFKVYKNTM 61

Query: 63  LEQRAEFLEAIATQIEALGDALIDRAVIETGLPKARIQGERGRTCTQLRTFARTVRAGEW 122
              +A+FL AIA +I ALGD LI+RAV E+GLP  RI GE GRT  QLR FA  V  G W
Sbjct: 62  PATKAKFLRAIANEIAALGDVLINRAVAESGLPVGRIIGEMGRTTGQLRMFADMVEEGSW 121

Query: 123 LDVRIDSALPERQPLPRADLRQRQVALGPVAVFGASNFPLAFSVAGGDTASALAAGCPVV 182
           +D  ID+A  +R P+PR+D+R+   A+GPV VFGASNFPLAFSVAGGDTASALAAGCPV+
Sbjct: 122 VDAVIDTAQLDRVPIPRSDIRRMLTAIGPVVVFGASNFPLAFSVAGGDTASALAAGCPVI 181

Query: 183 VKAHSAHPGTSELVGQAVAQAVKQCGLPEGVFSLLYGSGREVGIALVSDPRIKAVGFTGS 242
           VK H AHPGTS LVG A+++A K+ G+P+GVFSLL+ SG  VG ALV   + KAV FTGS
Sbjct: 182 VKVHPAHPGTSALVGAAISKAAKETGMPDGVFSLLFDSGYTVGAALVKHEQTKAVAFTGS 241

Query: 243 RSGGMALCQAAQARPEPIPVYAEMSSINPVFLFDAALQARAEALAQGFVASLTQGAGQFC 302
             GGMAL + AQ R   IPV+ EM SINPV L    L A+ E L   +  S+T GAGQFC
Sbjct: 242 YKGGMALIKLAQERKSLIPVFTEMGSINPVVLLPGILDAQPEVLVAKYAGSITLGAGQFC 301

Query: 303 TNPGLVIARQGPALQRFITAAAGYVQQGAAQTMLTPGIFSAY-QAGIAALADNPHAQAIT 361
           TNPGL++A +   L RFITA  G ++   + TMLTPGI+  Y       LA+N       
Sbjct: 302 TNPGLILAIRSAGLDRFITALGGAIELVPSATMLTPGIWKNYGTLAEETLAENGIELIAK 361

Query: 362 SGQAG-QGPNQCQAQLFVTQAEAFLADPALQAEVFGAASLVVACTDDEQVRQVAEHLEGQ 420
           S     +  NQ  A +    A+ F+A+     E+FG  SL+V   D  ++ QV   L+GQ
Sbjct: 362 SKLINTEKVNQSVATVATVSAKNFIANKKFSEEIFGPWSLLVVADDIAELEQVIASLDGQ 421

Query: 421 LTATLQLDEADIDSARALLPTLERKAGRILVNGWPTGVEVCDAMVHGGPFPATSDARTTS 480
           LT T+   + ++    ++L  L   +GR+++NG PTGVEVC AM HGGPFP+TSD+R TS
Sbjct: 422 LTTTVMAQKEELPQYTSVLNALTEISGRVILNGVPTGVEVCAAMQHGGPFPSTSDSRFTS 481

Query: 481 VGTAAILRFLRPVCYQDVPDALLPQALKHGNPLQLRR 517
           VGT AI RF+RPV +QD  D+LLP  L+  NPL + R
Sbjct: 482 VGTGAIYRFVRPVAWQDWDDSLLPPELQSNNPLNIWR 518


Lambda     K      H
   0.319    0.134    0.391 

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: 646
Number of extensions: 20
Number of successful extensions: 2
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: 525
Length of database: 527
Length adjustment: 35
Effective length of query: 490
Effective length of database: 492
Effective search space:   241080
Effective search space used:   241080
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 (21.8 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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