GapMind for catabolism of small carbon sources

 

Alignments for a candidate for manA in Pseudomonas fluorescens FW300-N1B4

Align alginate biosynthesis protein AlgA; EC 2.7.7.13; EC 5.3.1.8 (characterized)
to candidate Pf1N1B4_993 Mannose-1-phosphate guanylyltransferase (GDP) (EC 2.7.7.22) / Mannose-6-phosphate isomerase (EC 5.3.1.8)

Query= CharProtDB::CH_121570
         (483 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_993
          Length = 483

 Score =  912 bits (2356), Expect = 0.0
 Identities = 445/483 (92%), Positives = 466/483 (96%)

Query: 1   MIPVILSGGSGSRLWPLSRKQFPKQFLALTGEHTLFQQTLERLVFEGMDTPIVVCNKDHR 60
           MIPVILSGGSGSRLWPLSRKQFPKQFLALTGEHTLFQQTLERLVFEGMDTPIVVCNK+HR
Sbjct: 1   MIPVILSGGSGSRLWPLSRKQFPKQFLALTGEHTLFQQTLERLVFEGMDTPIVVCNKEHR 60

Query: 61  FIVNEQLANRKLECQRILMEPFGRNTAPAVALTAMMLVNEGRDELMLVLPADHVIDDQKA 120
           FIVNEQL+ R L+ QR+LMEPFGRNT+PAVALTAMMLVNEGRDELMLVLPADHV++DQKA
Sbjct: 61  FIVNEQLSARNLDVQRVLMEPFGRNTSPAVALTAMMLVNEGRDELMLVLPADHVLEDQKA 120

Query: 121 LQRALALATVAAERGEMVLFGVPATRPETGYGYIKSTNDSLLPEGVSRVQQFVEKPDEKR 180
           LQRALALATVAAERGEMVLFGVPAT+PETGYGYIKSTND+LLPEGVSRV  FVEKPD KR
Sbjct: 121 LQRALALATVAAERGEMVLFGVPATKPETGYGYIKSTNDALLPEGVSRVSHFVEKPDVKR 180

Query: 181 AVEFVKSGGYFWNSGMFLFRASRFLEELKKHDPDIYDTCVLTLERSEQTADTVTLDDATF 240
           A EFV+SGGYFWNSGMFLFRASRFLEELKKHDPDIYDTCVLTLERS Q ADTV +D ATF
Sbjct: 181 ATEFVQSGGYFWNSGMFLFRASRFLEELKKHDPDIYDTCVLTLERSAQDADTVDIDPATF 240

Query: 241 ACCPDNSIDYAVMEKTQRACVVPLSAGWSDVGCWASLWAVNDKDIHGNVSKGDVVIQDSR 300
           ACCPDNSIDY+VMEKTQRACVVPL+AGWSDVGCW+SLW VN+KD +GNV+KGDVVIQDS+
Sbjct: 241 ACCPDNSIDYSVMEKTQRACVVPLTAGWSDVGCWSSLWEVNEKDANGNVTKGDVVIQDSK 300

Query: 301 NCMIHGNGKLVSVIGLDNIVVVETKDAMMIAHKDKVQGVKQMVSTLNDQGRSETQNHCEV 360
           NCMIHGNGKLVSVIGL+NIVVVETKDAMMIAHKDKVQGVKQMV+TLN QGRSETQ HCEV
Sbjct: 301 NCMIHGNGKLVSVIGLENIVVVETKDAMMIAHKDKVQGVKQMVNTLNAQGRSETQTHCEV 360

Query: 361 YRPWGSYDSVDMGGRFQVKHISVKPGACLSLQMHHHRAEHWIVVSGTAEVTCDENVFLLT 420
           YRPWGSYDSVDMGGRFQVK ISVKPGACLSLQMHHHRAEHWIVVSGTAEVTCDENVFLLT
Sbjct: 361 YRPWGSYDSVDMGGRFQVKRISVKPGACLSLQMHHHRAEHWIVVSGTAEVTCDENVFLLT 420

Query: 421 ENQSTYIPIASVHRLRNPGKIPLEIIEVQSGSYLGEDDIERFEDIYGRSTPVERGVSVKT 480
           ENQSTYIPIASVHRLRNPGKIPLEIIEVQSGSYLGEDDIERFEDIYGRS P+ERGVSVKT
Sbjct: 421 ENQSTYIPIASVHRLRNPGKIPLEIIEVQSGSYLGEDDIERFEDIYGRSNPIERGVSVKT 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: 898
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:

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