GapMind for catabolism of small carbon sources

 

Alignments for a candidate for manP in Pseudomonas stutzeri RCH2

Align protein-Npi-phosphohistidine-D-mannose phosphotransferase (EC 2.7.1.191) (characterized)
to candidate GFF3289 Psest_3353 PTS system, fructose-specific, IIB component/PTS system, fructose subfamily, IIC component

Query= BRENDA::O31645
         (650 letters)



>FitnessBrowser__psRCH2:GFF3289
          Length = 579

 Score =  380 bits (977), Expect = e-110
 Identities = 197/461 (42%), Positives = 299/461 (64%), Gaps = 15/461 (3%)

Query: 2   KLLAITSCPNGIAHTYMAAENLQKAADRLGVSIKVETQGGIGVENKLTEEEIREADAIII 61
           KL+A+T+CP G+AHT+MAAE LQ+AA R G  ++VET+G +G  N L  + I  AD +++
Sbjct: 119 KLVAVTACPTGVAHTFMAAEALQQAAIRKGYDLQVETRGSVGARNVLEADVIAAADVVLL 178

Query: 62  AADRSVNKDRFIGKKLLSVGVQDGIRKPEELIQKALNGDIPVYRSATKSESGNHQEKKQN 121
           AAD  V+  RF GK++   G    +++PE  + +AL     +  +A  + +   ++ ++ 
Sbjct: 179 AADIEVDVARFAGKRVFRCGTGVALKQPEATLDRALEEGAVLSGNAVATSASGEKKGEKT 238

Query: 122 PIYRHLMNGVSFMVPFIVVGGLLIAVALTLGGEKTPKGLVIPDDSFWKTIEQIGS-ASFS 180
            +Y+H++ GVS+M+P +V GGLLIA++   G E   +     + +    + +IG   +F 
Sbjct: 239 GVYKHMLTGVSYMLPMVVAGGLLIALSFVFGIEAFKE-----EGTLAAALMKIGGETAFQ 293

Query: 181 FMIPILAGYIAYSIADKPGLVPGMIGGYIAATGSFYDSASGAGFLGGIIAGFLAGYAALW 240
            M+P+LAGYIAYSIAD+PGL PGMIGG +A T        GAGF+GGIIAGF+AGYAA  
Sbjct: 294 LMVPLLAGYIAYSIADRPGLAPGMIGGLLAGT-------LGAGFIGGIIAGFVAGYAAKA 346

Query: 241 IKK-LKVPKAIQPIMPIIIIPVFASLIVGLAFVFLIGAPVAQIFASLTVWLAGMKGSSSI 299
           + + + +P +I+ + PI+IIP+ ASL+ GL  ++++G PVA++ A LT +L  M  S++I
Sbjct: 347 VSRWIPLPASIESLKPILIIPLLASLVTGLVMIYIVGTPVAKLLAGLTEFLDTMGTSNAI 406

Query: 300 LLALILGAMISFDMGGPVNKVAFLFGSAMIGEGNYEIMGPIAVAICIPPIGLGIATFLGK 359
           LL L+LG M+  D+GGPVNK A+ F   ++   +Y  M     A  +PPIG+GIAT + +
Sbjct: 407 LLGLLLGTMMCVDLGGPVNKAAYAFSVGLLASQSYAPMAATMAAGMVPPIGMGIATLIAR 466

Query: 360 RKFEASQREMGKAAFTMGLFGITEGAIPFAAQDPLRVIPSIMAGSMTGSVIAMIGNVGDR 419
           RKF  ++RE GKAA  +G   I+EGAIPFAA+DPLRVIP+ +AG      ++M       
Sbjct: 467 RKFAQTEREAGKAALVLGCCFISEGAIPFAAKDPLRVIPASIAGGALTGALSMAFGAKLL 526

Query: 420 VAHGGPIVAVL-GAVDHVLMFFIAVIAGSLVTALFVNVLKK 459
             HGG  V ++  A++H L++ +A++AGSLVT +   V+K+
Sbjct: 527 APHGGLFVLLIPNAINHALLYLVAILAGSLVTGVIYAVIKQ 567



 Score = 59.7 bits (143), Expect = 4e-13
 Identities = 29/96 (30%), Positives = 51/96 (53%)

Query: 1  MKLLAITSCPNGIAHTYMAAENLQKAADRLGVSIKVETQGGIGVENKLTEEEIREADAII 60
          M LL +T+CPNG+  + + +  L+ AA RLG S  VE      + + LT  +I  AD ++
Sbjct: 1  MNLLIVTACPNGMVTSVLTSRLLEAAAHRLGWSTAVEVHDPKAIGSPLTPAQIANADLVV 60

Query: 61 IAADRSVNKDRFIGKKLLSVGVQDGIRKPEELIQKA 96
          +     ++  RF+GK++      + +  PE  ++ A
Sbjct: 61 VVKTGPLSLQRFVGKRVAQSTPSEALLDPEAFLRSA 96


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: 811
Number of extensions: 46
Number of successful extensions: 5
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:

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