GapMind for catabolism of small carbon sources

 

Alignments for a candidate for manA in Pseudomonas stutzeri RCH2

Align mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) (characterized)
to candidate GFF1782 Psest_1821 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase

Query= BRENDA::P07874
         (481 letters)



>FitnessBrowser__psRCH2:GFF1782
          Length = 469

 Score =  560 bits (1444), Expect = e-164
 Identities = 275/471 (58%), Positives = 353/471 (74%), Gaps = 7/471 (1%)

Query: 1   MIPVILSGGSGSRLWPLSRKQYPKQFLALTGDD-TLFQQTIKRLAFDGMQA--PLLVCNK 57
           ++PVI++GGSGSRLWPLSR+  PKQFLALT    ++ Q TI+RL  DG++A  PLL+CN+
Sbjct: 2   LLPVIIAGGSGSRLWPLSRQLNPKQFLALTDAQLSMLQSTIRRL--DGLEAGLPLLICNE 59

Query: 58  EHRFIVQEQLEAQNLASQAILLEPFGRNTAPAVAIAAMKLVAEGRDELLLILPADHVIED 117
           +HRF+  EQL   ++   +ILLEP GRNTAPA+A+AA++   EG D +LL+L ADH+I+D
Sbjct: 60  QHRFLAAEQLRQLSMEQASILLEPVGRNTAPAIALAALQATQEGDDPILLVLAADHLIQD 119

Query: 118 QRAFQQALALATNAAEKGEMVLFGIPASRPETGYGYIRASADAQLPEGVSRVQSFVEKPD 177
             AF  ++  A   A  G++V FGI  + PETGYGYI    +  L EG   V  FVEKP 
Sbjct: 120 VDAFHSSIQAAMPFATNGKLVTFGIVPTNPETGYGYIEKGKE--LGEGGFAVNRFVEKPS 177

Query: 178 EARAREFVAAGGYYWNSGMFLFRASRYLEELKKHDADIYDTCLLALERSQHDGDLVNIDA 237
              A E++A+G Y+WNSGMF+FRASRYL+EL++H   I   C  AL     D   V +DA
Sbjct: 178 LDIAEEYLASGEYFWNSGMFMFRASRYLDELERHQPSILAACRQALAAGTQDMHFVRVDA 237

Query: 238 ATFECCPDNSIDYAVMEKTSRACVVPLSAGWNDVGSWSSIWDVHAKDANGNVTKGDVLVH 297
           ATF  CP++S+DYAVMEKT+ A +VPL AGW+DVGSW+++W+   KDA GNV KGDVL H
Sbjct: 238 ATFAACPEDSVDYAVMEKTNDAVMVPLDAGWSDVGSWTALWEASNKDAEGNVFKGDVLGH 297

Query: 298 DSHNCLVHGNGKLVSVIGLEDIVVVETKDAMMIAHKDRVQDVKHVVKDLDAQGRSETQNH 357
            + N  VH + +LV+ +G+ED+V+VETKDA+++AHK++VQDVK +V+ + A  R E  NH
Sbjct: 298 ATRNSFVHADSRLVATLGVEDLVIVETKDAVLVAHKNQVQDVKKLVERIKADNRHEHLNH 357

Query: 358 CEVYRPWGSYDSVDMGGRFQVKHITVKPGARLSLQMHHHRAEHWIVVSGTAQVTCDDKTF 417
            EVYRPWG YD++D G R+QVK ITV+PGA+LS+QMHHHRAEHW+VVSGTA+VT  DKT+
Sbjct: 358 REVYRPWGVYDAIDSGHRYQVKRITVQPGAKLSVQMHHHRAEHWVVVSGTAKVTNGDKTY 417

Query: 418 LLTENQSTYIPIASVHRLANPGKIPLEIIEVQSGSYLGEDDIERLEDVYGR 468
           L+TENQSTYIP+  VH L NPG IPLE+IEVQSGSYLGEDDI R ED YGR
Sbjct: 418 LVTENQSTYIPVGQVHALENPGVIPLELIEVQSGSYLGEDDIVRFEDQYGR 468


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: 674
Number of extensions: 29
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: 469
Length adjustment: 33
Effective length of query: 448
Effective length of database: 436
Effective search space:   195328
Effective search space used:   195328
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