GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__psRCH2:GFF1782 Psest_1821 mannose-1-phosphate
           guanylyltransferase/mannose-6-phosphate isomerase
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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