GapMind for catabolism of small carbon sources

 

Alignments for a candidate for manA in Dechlorosoma suillum PS

Align mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) (characterized)
to candidate Dsui_0087 Dsui_0087 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase

Query= BRENDA::P07874
         (481 letters)



>FitnessBrowser__PS:Dsui_0087
          Length = 478

 Score =  435 bits (1119), Expect = e-126
 Identities = 227/473 (47%), Positives = 304/473 (64%), Gaps = 10/473 (2%)

Query: 4   VILSGGSGSRLWPLSRKQYPKQFLALTGDDTLFQQTIKRLAFDGMQAPLLVCNKEHRFIV 63
           VIL GGSG+RLWPLSRK +PKQF+ L GD +L Q T +R +  G +  L V  ++HRF+V
Sbjct: 9   VILCGGSGTRLWPLSRKSFPKQFVPLLGDKSLLQLTFERTSGLGERV-LAVAAEDHRFMV 67

Query: 64  QEQLEAQNLASQAILLEPFGRNTAPAVAIAAMKLVAEGRDELLLILPADHVIEDQRAFQQ 123
            + + A  +A  A++LEP  RNTA A+A+AA++ + +G D LLL  PADH + D   F +
Sbjct: 68  TDDMLAARVAG-AVILEPAARNTAAAMALAALQAIQDGLD-LLLFCPADHHVPDVEGFLR 125

Query: 124 ALALATNAAEKGEMVLFGIPASRPETGYGYIRASADAQLPEGVSRVQSFVEKPDEARARE 183
            +     AA+ G +V FG+  S P T YGYI+        +G      F+EKPD ARA+E
Sbjct: 126 TIRQGVPAAQAGALVTFGVVPSFPSTAYGYIQRGDSRA--DGSFHAGRFIEKPDLARAQE 183

Query: 184 FVAAGGYYWNSGMFLFRASRYLEELKKHDADIYDTCLLALERSQHDGD-----LVNIDAA 238
            + AG   WN+G+FL RA   LE L+ H  DI  TC  A+  +Q +        V  +A 
Sbjct: 184 LLLAGDNLWNAGIFLCRAVILLEALEAHAPDILLTCRQAMADAQVEVSPSGHAFVRPEAR 243

Query: 239 TFECCPDNSIDYAVMEKTSRACVVPLSAGWNDVGSWSSIWDVHAKDANGNVTKGDVLVHD 298
           +F  C   SIDYAVME+     VVP    W+DVGSW+++ D+   D +GN   G  +VH 
Sbjct: 244 SFGTCRSQSIDYAVMEQHDNVAVVPFEGQWSDVGSWNAVADLQVPDGDGNRVAGQGMVHH 303

Query: 299 SHNCLVHGNGKLVSVIGLEDIVVVETKDAMMIAHKDRVQDVKHVVKDLDAQGRSETQNHC 358
           S N  +H   + V  +G +++++++T DA+++AH+D+ + VK VV  L+    ++   H 
Sbjct: 304 SSNTFIHAPHRPVVALGTDNLLIIDTPDAVLVAHRDKAEQVKDVVTRLEQAQCTQAVTHR 363

Query: 359 EVYRPWGSYDSVDMGGRFQVKHITVKPGARLSLQMHHHRAEHWIVVSGTAQVTCDDKTFL 418
           +V RPWG YDS+D G RFQVK I VKPGA LSLQ HHHRAEHW+VV GTA+VTC + TFL
Sbjct: 364 KVARPWGWYDSIDRGERFQVKRIGVKPGASLSLQKHHHRAEHWVVVKGTAEVTCGENTFL 423

Query: 419 LTENQSTYIPIASVHRLANPGKIPLEIIEVQSGSYLGEDDIERLEDVYGRTAE 471
           L+ENQSTYIPI  VHRL NPG + LEI+E+QSGSYLGEDDI RL D YGR  +
Sbjct: 424 LSENQSTYIPIGEVHRLRNPGVVELEIVEIQSGSYLGEDDIVRLHDTYGRAPQ 476


Lambda     K      H
   0.319    0.134    0.400 

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: 662
Number of extensions: 33
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: 481
Length of database: 478
Length adjustment: 34
Effective length of query: 447
Effective length of database: 444
Effective search space:   198468
Effective search space used:   198468
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: 51 (24.3 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