GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__psRCH2:GFF3289 Psest_3353 PTS system,
           fructose-specific, IIB component/PTS system, fructose
           subfamily, IIC component
          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 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