GapMind for catabolism of small carbon sources

 

Aligments for a candidate for manP in Pseudomonas fluorescens FW300-N2E3

Align protein-Npi-phosphohistidine-D-mannose phosphotransferase (EC 2.7.1.191) (characterized)
to candidate AO353_05475 AO353_05475 PTS fructose transporter subunit IIBC

Query= BRENDA::O31645
         (650 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_05475 AO353_05475 PTS
           fructose transporter subunit IIBC
          Length = 579

 Score =  382 bits (981), Expect = e-110
 Identities = 206/472 (43%), Positives = 303/472 (64%), Gaps = 24/472 (5%)

Query: 2   KLLAITSCPNGIAHTYMAAENLQKAADRLGVSIKVETQGGIGVENKLTEEEIREADAIII 61
           +L+A+T+CP G+AHT+MAAE LQ+AA RLG  ++VETQG +G  N L+ + I +AD +++
Sbjct: 121 RLVAVTACPTGVAHTFMAAEALQQAAKRLGYDLQVETQGSVGARNPLSAQAIADADVVLL 180

Query: 62  AADRSVNKDRFIGKKLLSVGVQDGIRKPEELIQKAL-NGDIPVYRSATKSESGNHQEKKQ 120
           AAD  V  +RF GKK+   G    +++ E  + KAL  G      S  +  +    +K++
Sbjct: 181 AADIEVATERFAGKKIYRCGTGIALKQAEATLNKALAEGKQETASSGVQGPA----KKEK 236

Query: 121 NPIYRHLMNGVSFMVPFIVVGGLLIAVALTLG--GEKTPKGLVIPDDSFWKTIEQIGS-A 177
             +Y+HL+ GVSFM+P +V GGL+IA++   G    K P  L          + QIG   
Sbjct: 237 TGVYKHLLTGVSFMLPMVVAGGLMIALSFVFGITAFKEPGTLAA-------ALMQIGGDT 289

Query: 178 SFSFMIPILAGYIAYSIADKPGLVPGMIGGYIAATGSFYDSASGAGFLGGIIAGFLAGYA 237
           +F  M+P+LAGYIAYSIAD+PGL PGMIGG +A+T        GAGF+GGIIAGF+AGYA
Sbjct: 290 AFKLMVPLLAGYIAYSIADRPGLAPGMIGGLLAST-------LGAGFIGGIIAGFIAGYA 342

Query: 238 ALWIKKL-KVPKAIQPIMPIIIIPVFASLIVGLAFVFLIGAPVAQIFASLTVWLAGMKGS 296
           A  I +  ++P++++ + PI+IIP+ ASL  GL  ++++G PVA +  SLT +L  M  +
Sbjct: 343 AQAINRYARLPQSLEALKPILIIPLLASLFTGLVMIYVVGKPVAGLLESLTHFLDSMGTT 402

Query: 297 SSILLALILGAMISFDMGGPVNKVAFLFGSAMIGEGNYEIMGPIAVAICIPPIGLGIATF 356
           ++ILL ++LG M+  D+GGP+NK A+ F   ++   +Y  M     A  +PPIGLGIATF
Sbjct: 403 NAILLGVLLGGMMCVDLGGPINKAAYAFSVGLLASQSYAPMAATMAAGMVPPIGLGIATF 462

Query: 357 LGKRKFEASQREMGKAAFTMGLFGITEGAIPFAAQDPLRVIPSIMAGSMTGSVIAMIGNV 416
           + +RKF  ++RE GKAA  +GL  I+EGAIPFAA+DPLRVIP+ +AG      ++M    
Sbjct: 463 IARRKFAQTEREAGKAALVLGLCFISEGAIPFAAKDPLRVIPASIAGGALAGALSMYFGC 522

Query: 417 GDRVAHGGPIVAVL-GAVDHVLMFFIAVIAGSLVTALFVNVLKKDITASPVL 467
                HGG  V ++  A++H L++ +A++AGSL+TA+    +K+   A   L
Sbjct: 523 KLMAPHGGLFVMLIPNAINHALLYLLAIVAGSLLTAVVYAAVKRPEVAELAL 574



 Score = 53.9 bits (128), Expect = 2e-11
 Identities = 25/95 (26%), Positives = 51/95 (53%)

Query: 1  MKLLAITSCPNGIAHTYMAAENLQKAADRLGVSIKVETQGGIGVENKLTEEEIREADAII 60
          MKL  +T+CPNG+  + + A  L  AA R G S  VE       E +L+   + +A+ ++
Sbjct: 1  MKLAIVTACPNGMVTSVLCARLLDAAAQRQGWSTSVEVHDAAHPERQLSAATLEDAEWVL 60

Query: 61 IAADRSVNKDRFIGKKLLSVGVQDGIRKPEELIQK 95
          + +  +V+  RF+GK++        ++  + ++++
Sbjct: 61 LVSTGTVDMSRFVGKRVFQSTPSQALQDVDAVLRR 95


Lambda     K      H
   0.319    0.137    0.386 

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: 770
Number of extensions: 45
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 650
Length of database: 579
Length adjustment: 37
Effective length of query: 613
Effective length of database: 542
Effective search space:   332246
Effective search space used:   332246
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 (21.7 bits)
S2: 53 (25.0 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