GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Keio:16157
          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.

Links

Downloads

Related tools

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