GapMind for catabolism of small carbon sources

 

Alignments for a candidate for manA in Pseudomonas fluorescens FW300-N2E3

Align mannose-1-phosphate guanylyltransferase (EC 2.7.7.13) (characterized)
to candidate AO353_10250 AO353_10250 mannose-1-phosphate guanylyltransferase

Query= BRENDA::P07874
         (481 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_10250
          Length = 480

 Score =  377 bits (968), Expect = e-109
 Identities = 204/478 (42%), Positives = 294/478 (61%), Gaps = 11/478 (2%)

Query: 1   MIPVILSGGSGSRLWPLSRKQYPKQFLALTGDDTLFQQTIKRLA-FDGMQAPLL-VCNKE 58
           +IPVILSGG+G+RLWP+SR+ +PK F+ L    TL  +T +R A   G    ++ V N++
Sbjct: 2   LIPVILSGGAGTRLWPVSREGHPKPFMTLPDGQTLLGKTYQRAAGLLGTHGDIVTVTNRD 61

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

Query: 116 EDQRAFQQALALATNAAEKGEMVLFGIPASRPETGYGYIRASADAQLPEGVSRVQSFVEK 175
           +++ AF+ A+  A   AE G +V FG+  + PETG+GYI         +G ++V  FVEK
Sbjct: 122 QNEDAFKTAVRHAVKLAEAGHLVTFGVIPTAPETGFGYIERGEPLD-EQGATKVARFVEK 180

Query: 176 PDEARAREFVAAGGYYWNSGMFLFRASRYLEELKKHDADIY---DTCLLALERSQHDGDL 232
           PD   A  ++ +G + WNSGMF F     L +L+ H   +    D CL A    +  G L
Sbjct: 181 PDLQTAMHYLESGNFLWNSGMFCFSVGTLLAQLQLHAPQLLEQADACLAASTTVETGGCL 240

Query: 233 VN-IDAATFECCPDNSIDYAVMEKTSRACVVPLSAGWNDVGSWSSIWDVHAKDANGNVTK 291
              + A  F    D SIDYA+ME++++  V+P     + +GSW ++  + A DA  N   
Sbjct: 241 QQELSATHFAEMTDISIDYALMERSNKVVVIPAGFDCSGIGSWGAVSALVAADAQNNRAS 300

Query: 292 GDVLVHDSHNCLVHGNGKLVSVIGLEDIVVVETKDAMMIAHKDRVQDVKHVVKDLDAQGR 351
           GD L  DSHN  V  +G++V+ +G+++++V++T DA+++AH DR QDV+ VVK L  +  
Sbjct: 301 GDALFIDSHNNFVQSDGRMVATVGVDNLIVIDTADAVLVAHTDRAQDVRKVVKQLKEKEH 360

Query: 352 SETQNHCEVYRPWGSYDSVDMGGRFQVKHITVKPGARLSLQMHHHRAEHWIVVSGTAQVT 411
                H  V RPWG+Y  ++ G RF++K I VK GA+LSLQMHHHR EHW+   G A+VT
Sbjct: 361 ESYSLHRTVSRPWGTYTVLEEGPRFKIKRIVVKSGAKLSLQMHHHRNEHWVEAEGMAKVT 420

Query: 412 CDDK-TFLLTENQSTYIPIASVHRLANPGKIPLEIIEVQSGSYLGEDDIERLEDVYGR 468
            +   + L+ +N+ST+I     HRL NPG I L IIEVQSG YLGEDDI R ED YGR
Sbjct: 421 NNGSGSRLVAKNESTFIAAGHKHRLENPGVIDLVIIEVQSGEYLGEDDIVRFEDQYGR 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: 582
Number of extensions: 32
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: 480
Length adjustment: 34
Effective length of query: 447
Effective length of database: 446
Effective search space:   199362
Effective search space used:   199362
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