GapMind for catabolism of small carbon sources

 

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

Align alginate biosynthesis protein AlgA; EC 2.7.7.13; EC 5.3.1.8 (characterized)
to candidate AO353_04735 AO353_04735 mannose-1-phosphate guanylyltransferase

Query= CharProtDB::CH_121570
         (483 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_04735
          Length = 483

 Score =  922 bits (2384), Expect = 0.0
 Identities = 449/483 (92%), Positives = 471/483 (97%)

Query: 1   MIPVILSGGSGSRLWPLSRKQFPKQFLALTGEHTLFQQTLERLVFEGMDTPIVVCNKDHR 60
           MIPVILSGGSGSRLWPLSRKQFPKQFLALTGE TLFQQTLERLVFEGMD+PIVVCNKDHR
Sbjct: 1   MIPVILSGGSGSRLWPLSRKQFPKQFLALTGEQTLFQQTLERLVFEGMDSPIVVCNKDHR 60

Query: 61  FIVNEQLANRKLECQRILMEPFGRNTAPAVALTAMMLVNEGRDELMLVLPADHVIDDQKA 120
           FIVNEQL+NRKLE QRILMEPFGRNTAPAVA+TAMMLVNEGRDELMLVLPADHV++DQKA
Sbjct: 61  FIVNEQLSNRKLEAQRILMEPFGRNTAPAVAMTAMMLVNEGRDELMLVLPADHVLEDQKA 120

Query: 121 LQRALALATVAAERGEMVLFGVPATRPETGYGYIKSTNDSLLPEGVSRVQQFVEKPDEKR 180
           LQRALALATVAAERGEMVLFGVPAT+PETGYGYIKS ND+LLPEGVSRV  FVEKPD KR
Sbjct: 121 LQRALALATVAAERGEMVLFGVPATKPETGYGYIKSANDALLPEGVSRVSHFVEKPDVKR 180

Query: 181 AVEFVKSGGYFWNSGMFLFRASRFLEELKKHDPDIYDTCVLTLERSEQTADTVTLDDATF 240
           A EFV++GGYFWNSGMFLFRASRFLEELKKHDPDIYDTC+LTLERSEQ ADT+T D+ATF
Sbjct: 181 ATEFVEAGGYFWNSGMFLFRASRFLEELKKHDPDIYDTCLLTLERSEQDADTITFDEATF 240

Query: 241 ACCPDNSIDYAVMEKTQRACVVPLSAGWSDVGCWASLWAVNDKDIHGNVSKGDVVIQDSR 300
           ACCPDNSIDYAVMEKT+RACVVPLSAGWSDVGCW+SLW V++KD +GNV+KGDVVIQDSR
Sbjct: 241 ACCPDNSIDYAVMEKTRRACVVPLSAGWSDVGCWSSLWDVHEKDANGNVTKGDVVIQDSR 300

Query: 301 NCMIHGNGKLVSVIGLDNIVVVETKDAMMIAHKDKVQGVKQMVSTLNDQGRSETQNHCEV 360
           NCMIHGNGKLVSVIGL+NIVVVETKDAMMIAHKDKVQGVKQMV+TLN+QGRSETQNHCEV
Sbjct: 301 NCMIHGNGKLVSVIGLENIVVVETKDAMMIAHKDKVQGVKQMVNTLNEQGRSETQNHCEV 360

Query: 361 YRPWGSYDSVDMGGRFQVKHISVKPGACLSLQMHHHRAEHWIVVSGTAEVTCDENVFLLT 420
           YRPWGSYDSVDMGGRFQVKHISVKPGACLSLQMHHHRAEHWIVVSGTAEVTCDENVFLL 
Sbjct: 361 YRPWGSYDSVDMGGRFQVKHISVKPGACLSLQMHHHRAEHWIVVSGTAEVTCDENVFLLC 420

Query: 421 ENQSTYIPIASVHRLRNPGKIPLEIIEVQSGSYLGEDDIERFEDIYGRSTPVERGVSVKT 480
           ENQSTYIPIASVHRLRNPGKIPLEIIEVQSGSYLGEDDIERFEDIYGRSTP+ERGVSVKT
Sbjct: 421 ENQSTYIPIASVHRLRNPGKIPLEIIEVQSGSYLGEDDIERFEDIYGRSTPIERGVSVKT 480

Query: 481 IAQ 483
           IAQ
Sbjct: 481 IAQ 483


Lambda     K      H
   0.319    0.135    0.405 

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: 910
Number of extensions: 26
Number of successful extensions: 1
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: 483
Length of database: 483
Length adjustment: 34
Effective length of query: 449
Effective length of database: 449
Effective search space:   201601
Effective search space used:   201601
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