GapMind for catabolism of small carbon sources

 

Aligments for a candidate for manA in Escherichia coli BW25113

Align mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) (characterized)
to candidate 16157 b2049 mannose-1-phosphate guanyltransferase (NCBI)

Query= BRENDA::P07874
         (481 letters)



>lcl|FitnessBrowser__Keio:16157 b2049 mannose-1-phosphate
           guanyltransferase (NCBI)
          Length = 478

 Score =  520 bits (1338), Expect = e-152
 Identities = 262/472 (55%), Positives = 337/472 (71%), Gaps = 4/472 (0%)

Query: 1   MIPVILSGGSGSRLWPLSRKQYPKQFLALTGDDTLFQQTIKRLAFDGMQAPLLVCNKEHR 60
           + PV+++GGSGSRLWPLSR  YPKQFL L GD T+ Q TI RL     ++P+++CN++HR
Sbjct: 6   LYPVVMAGGSGSRLWPLSRVLYPKQFLCLKGDLTMLQTTICRLNGVECESPVVICNEQHR 65

Query: 61  FIVQEQLEAQNLASQAILLEPFGRNTAPAVAIAAM--KLVAEGRDELLLILPADHVIEDQ 118
           FIV EQL   N  ++ I+LEP GRNTAPA+A+AA+  K  +   D L+L+L ADHVI D+
Sbjct: 66  FIVAEQLRQLNKLTENIILEPAGRNTAPAIALAALAAKRHSPESDPLMLVLAADHVIADE 125

Query: 119 RAFQQALALATNAAEKGEMVLFGIPASRPETGYGYIR-ASADAQLPEGVS-RVQSFVEKP 176
            AF+ A+  A   AE G++V FGI    PETGYGYIR     A   + V+  V  FVEKP
Sbjct: 126 DAFRAAVRNAMPYAEAGKLVTFGIVPDLPETGYGYIRRGEVSAGEQDMVAFEVAQFVEKP 185

Query: 177 DEARAREFVAAGGYYWNSGMFLFRASRYLEELKKHDADIYDTCLLALERSQHDGDLVNID 236
           +   A+ +VA+G YYWNSGMFLFRA RYLEELKK+  DI D C  A+     D + + +D
Sbjct: 186 NLETAQAYVASGEYYWNSGMFLFRAGRYLEELKKYRPDILDACEKAMSAVDPDLNFIRVD 245

Query: 237 AATFECCPDNSIDYAVMEKTSRACVVPLSAGWNDVGSWSSIWDVHAKDANGNVTKGDVLV 296
              F  CP+ S+DYAVME+T+ A VVP+ AGW+DVGSWSS+W++ A  A GNV  GDV+ 
Sbjct: 246 EEAFLACPEESVDYAVMERTADAVVVPMDAGWSDVGSWSSLWEISAHTAEGNVCHGDVIN 305

Query: 297 HDSHNCLVHGNGKLVSVIGLEDIVVVETKDAMMIAHKDRVQDVKHVVKDLDAQGRSETQN 356
           H + N  V+    LV+ +G++D+VVV+TKDA++IA ++ VQDVK VV+ + A GR E + 
Sbjct: 306 HKTENSYVYAESGLVTTVGVKDLVVVQTKDAVLIADRNAVQDVKKVVEQIKADGRHEHRV 365

Query: 357 HCEVYRPWGSYDSVDMGGRFQVKHITVKPGARLSLQMHHHRAEHWIVVSGTAQVTCDDKT 416
           H EVYRPWG YDS+D G R+QVK ITVKPG  LS+QMHHHRAEHW+VV+GTA+VT D   
Sbjct: 366 HREVYRPWGKYDSIDAGDRYQVKRITVKPGEGLSVQMHHHRAEHWVVVAGTAKVTIDGDI 425

Query: 417 FLLTENQSTYIPIASVHRLANPGKIPLEIIEVQSGSYLGEDDIERLEDVYGR 468
            LL EN+S YIP+ + H L NPGKIPL++IEV+SGSYL EDD+ R  D YGR
Sbjct: 426 KLLGENESIYIPLGATHCLENPGKIPLDLIEVRSGSYLEEDDVVRFADRYGR 477


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: 645
Number of extensions: 33
Number of successful extensions: 3
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 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