GapMind for catabolism of small carbon sources

 

Alignments for a candidate for manA in Pseudomonas fluorescens FW300-N2E2

Align mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) (characterized)
to candidate Pf6N2E2_4241 Mannose-1-phosphate guanylyltransferase (GDP) (EC 2.7.7.22)

Query= BRENDA::P07874
         (481 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4241
          Length = 483

 Score =  404 bits (1039), Expect = e-117
 Identities = 214/478 (44%), Positives = 305/478 (63%), Gaps = 11/478 (2%)

Query: 1   MIPVILSGGSGSRLWPLSRKQYPKQFLALTGDDTLFQQTIKRLA--FDGMQAPLLVCNKE 58
           +IPVILSGG+G+RLWP+SR+ +PK F+ L    +L  +T +R A  FDG    + V N+E
Sbjct: 2   LIPVILSGGAGTRLWPVSREGHPKPFMLLPDGQSLLGKTYRRAAGLFDGRGDIVTVTNRE 61

Query: 59  HRFIVQEQLEAQNLASQA--ILLEPFGRNTAPAVAIAAMKLVA-EGRDELLLILPADHVI 115
           + F  ++  ++ +L       +LEP GRNTAPA+A AA+ + A  G D +L+++PADH+I
Sbjct: 62  YYFQSRDHYQSAHLERHRGHFVLEPTGRNTAPAIATAALAVQALHGDDPILVVMPADHLI 121

Query: 116 EDQRAFQQALALATNAAEKGEMVLFGIPASRPETGYGYIRASADAQLPEGVSRVQSFVEK 175
           +D+ AFQ A+A A   A+ G +V FG+  S PETG+GYI         +G ++V  FVEK
Sbjct: 122 QDEAAFQTAVAHAVELAKNGHLVTFGVLPSTPETGFGYIERGKPLDT-KGAAKVVRFVEK 180

Query: 176 PDEARAREFVAAGGYYWNSGMFLFRASRYLEELKKHDADIYD---TCLLALERSQHDGDL 232
           PD   A +++ +G + WNSGMF F     L EL+ H  ++ +   TC+ A    +  G +
Sbjct: 181 PDLQTATQYLESGRFLWNSGMFCFSVKTLLAELQAHAPELLEQARTCVTASTAVETSGCV 240

Query: 233 VN-IDAATFECCPDNSIDYAVMEKTSRACVVPLSAGWNDVGSWSSIWDVHAKDANGNVTK 291
              + AA F   PD SIDYA+ME+++   V+P +  W+D+GSWS++  +   DA  N   
Sbjct: 241 QQELSAAHFAEMPDISIDYALMERSANVVVIPAAFDWSDIGSWSAVAGLVPADAQNNRAT 300

Query: 292 GDVLVHDSHNCLVHGNGKLVSVIGLEDIVVVETKDAMMIAHKDRVQDVKHVVKDLDAQGR 351
           G+ L  DS N  V  +G+LV+ +G+E +++++T DA+++AH DR QDV+ V + L  +  
Sbjct: 301 GEALFIDSQNNFVQSDGRLVAALGVEHLIIIDTADAVLVAHADRAQDVRRVARQLKDKDH 360

Query: 352 SETQNHCEVYRPWGSYDSVDMGGRFQVKHITVKPGARLSLQMHHHRAEHWIVVSGTAQVT 411
              + H  V RPWGSY  ++ G RF++K I VKPGA LSLQMHHHR EHW+VV G A+VT
Sbjct: 361 EAYRLHRTVSRPWGSYTVLEEGPRFKIKRIVVKPGASLSLQMHHHRNEHWVVVEGMAKVT 420

Query: 412 CDDK-TFLLTENQSTYIPIASVHRLANPGKIPLEIIEVQSGSYLGEDDIERLEDVYGR 468
            +   + L+ +N+ST+IP    HRL NPG I L IIEVQSG YLGEDDI R ED YGR
Sbjct: 421 NNGSGSHLVAKNESTFIPAGHKHRLENPGVIDLVIIEVQSGEYLGEDDIVRFEDHYGR 478


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: 637
Number of extensions: 39
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: 483
Length adjustment: 34
Effective length of query: 447
Effective length of database: 449
Effective search space:   200703
Effective search space used:   200703
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: 52 (24.6 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