GapMind for catabolism of small carbon sources

 

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

Align alginate biosynthesis protein AlgA; EC 2.7.7.13; EC 5.3.1.8 (characterized)
to candidate Pf6N2E2_5377 Mannose-6-phosphate isomerase (EC 5.3.1.8) / Mannose-1-phosphate guanylyltransferase (GDP) (EC 2.7.7.22)

Query= CharProtDB::CH_121570
         (483 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5377 Mannose-6-phosphate
           isomerase (EC 5.3.1.8) / Mannose-1-phosphate
           guanylyltransferase (GDP) (EC 2.7.7.22)
          Length = 483

 Score =  931 bits (2406), Expect = 0.0
 Identities = 453/483 (93%), Positives = 472/483 (97%)

Query: 1   MIPVILSGGSGSRLWPLSRKQFPKQFLALTGEHTLFQQTLERLVFEGMDTPIVVCNKDHR 60
           MIPVILSGGSGSRLWPLSRKQFPKQFLALTGEHTLFQQTLERLVFEGMDTPIVVCNKDHR
Sbjct: 1   MIPVILSGGSGSRLWPLSRKQFPKQFLALTGEHTLFQQTLERLVFEGMDTPIVVCNKDHR 60

Query: 61  FIVNEQLANRKLECQRILMEPFGRNTAPAVALTAMMLVNEGRDELMLVLPADHVIDDQKA 120
           FIVNEQL+NRKLE QRILMEPFGRNTAPAVALTAMMLVNEGRDELMLVLPADHVI+DQKA
Sbjct: 61  FIVNEQLSNRKLEAQRILMEPFGRNTAPAVALTAMMLVNEGRDELMLVLPADHVIEDQKA 120

Query: 121 LQRALALATVAAERGEMVLFGVPATRPETGYGYIKSTNDSLLPEGVSRVQQFVEKPDEKR 180
           LQRALALATVAAERGEMVLFG+P T+PETGYGYIKSTND+LLPEGVSRV  FVEKPD KR
Sbjct: 121 LQRALALATVAAERGEMVLFGIPPTKPETGYGYIKSTNDALLPEGVSRVSHFVEKPDAKR 180

Query: 181 AVEFVKSGGYFWNSGMFLFRASRFLEELKKHDPDIYDTCVLTLERSEQTADTVTLDDATF 240
           A EF+++GGYFWNSGMFLFRASRFLEELKKHDPDIYDTC+LTLERSEQTADT+T D+ATF
Sbjct: 181 ATEFLEAGGYFWNSGMFLFRASRFLEELKKHDPDIYDTCLLTLERSEQTADTITFDEATF 240

Query: 241 ACCPDNSIDYAVMEKTQRACVVPLSAGWSDVGCWASLWAVNDKDIHGNVSKGDVVIQDSR 300
           ACCPDNSIDYAVMEKTQRACVVPL+AGWSDVGCWASLW VN+KD +GNV+KGDVVIQDSR
Sbjct: 241 ACCPDNSIDYAVMEKTQRACVVPLAAGWSDVGCWASLWEVNEKDTNGNVTKGDVVIQDSR 300

Query: 301 NCMIHGNGKLVSVIGLDNIVVVETKDAMMIAHKDKVQGVKQMVSTLNDQGRSETQNHCEV 360
           NCMIHGNGKLVSVIGL+NIVVVETKDAMMIAHKDKVQGVKQMV+TLN QGR+ETQNHCEV
Sbjct: 301 NCMIHGNGKLVSVIGLENIVVVETKDAMMIAHKDKVQGVKQMVNTLNAQGRTETQNHCEV 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: 906
Number of extensions: 25
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 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