GapMind for catabolism of small carbon sources

 

Aligments for a candidate for manP in Marinobacter adhaerens HP15

Align protein-Npi-phosphohistidine-D-mannose phosphotransferase (EC 2.7.1.191) (characterized)
to candidate GFF3783 HP15_3725 PTS system, fructose-specific IIBC component

Query= BRENDA::O31645
         (650 letters)



>lcl|FitnessBrowser__Marino:GFF3783 HP15_3725 PTS system,
           fructose-specific IIBC component
          Length = 587

 Score =  377 bits (969), Expect = e-109
 Identities = 207/462 (44%), Positives = 297/462 (64%), Gaps = 18/462 (3%)

Query: 2   KLLAITSCPNGIAHTYMAAENLQKAADRLGVSIKVETQGGIGVENKLTEEEIREADAIII 61
           +++A+T+CP G+AHT+MAAE L  AA   G  I+VETQG +G ++ LTEEEI  AD +I+
Sbjct: 128 RIVAVTACPTGVAHTFMAAEALTAAAQSAGHKIRVETQGSVGAQDPLTEEEIAAADVVIL 187

Query: 62  AADRSVNKDRFIGKKLLSVGVQDGIRKPEELIQKALNGDIPVYRSATKSESGNHQEKKQN 121
           A D  V+  RF GK++        ++KP + I+ AL   + +     K+   +   +K+ 
Sbjct: 188 ACDIEVDPGRFSGKRVWRTSTGAALKKPADTIRDALEQAVVLNAGQKKTSGASGSGEKKG 247

Query: 122 PIYRHLMNGVSFMVPFIVVGGLLIAVALTLGGEKTPKGLVIPDDSFWKTIEQIGSAS-FS 180
           P Y+HL+ GVSFM+P +V GGLLIA++   G E   +     + +    + QIG  + F 
Sbjct: 248 P-YKHLLTGVSFMLPMVVAGGLLIALSFVFGIEAFQE-----EGTLAAALMQIGGGTAFK 301

Query: 181 FMIPILAGYIAYSIADKPGLVPGMIGGYIAATGSFYDSASGAGFLGGIIAGFLAGYAALW 240
            MIP+LAGYIA+SIAD+PGL PGMIGG++A          GAGFLGGI+AGFLAGY A +
Sbjct: 302 LMIPLLAGYIAWSIADRPGLAPGMIGGFLAGE-------LGAGFLGGIVAGFLAGYVARF 354

Query: 241 I-KKLKVPKAIQPIMPIIIIPVFASLIVGLAFVFLIGAPVAQIFASLTVWLAGMKGSSSI 299
           I +KL +P++I+ + PI+IIP+ ASL+ GL  +++IG P+A I  +LT +L GM  +++I
Sbjct: 355 ISQKLPMPESIESLKPILIIPLLASLVTGLGMIYVIGEPMAAIMGALTGFLEGMGTTNAI 414

Query: 300 LLALILGAMISFDMGGPVNKVAFLFGSAMI--GEGNYEIMGPIAVAICIPPIGLGIATFL 357
           LL  ILGAM+ FD+GGPVNK A+ FG  ++  G G    M  I  A  +P IG+G+A+F+
Sbjct: 415 LLGGILGAMMCFDLGGPVNKAAYTFGVGLLSEGSGGSAPMAAIMAAGMVPAIGMGVASFI 474

Query: 358 GKRKFEASQREMGKAAFTMGLFGITEGAIPFAAQDPLRVIPSIMAGSMTGSVIAMIGNVG 417
            +RKF  ++R+ G+A+F +GL  I+EGAIPF A+DPLRVIP  M G      ++M+  V 
Sbjct: 475 ARRKFAEAERQAGRASFVLGLCFISEGAIPFMAKDPLRVIPVCMIGGAITGALSMLFTVK 534

Query: 418 DRVAHGGP-IVAVLGAVDHVLMFFIAVIAGSLVTALFVNVLK 458
               HGG  ++A+  AV  VL + IA+  GSLV      +LK
Sbjct: 535 LMAPHGGLFVLAIPNAVSAVLPYLIAIAVGSLVIGFGYALLK 576



 Score = 72.0 bits (175), Expect = 7e-17
 Identities = 36/97 (37%), Positives = 61/97 (62%), Gaps = 1/97 (1%)

Query: 1  MKLLAITSCPNGIAHTYMAAENLQKAADRLGVSIKVETQGGIG-VENKLTEEEIREADAI 59
          M L+ +T+CP G+A  ++AA  L++AA+R G S+  +T+G  G  +NK +E  I++AD +
Sbjct: 1  MNLIIVTACPQGVATRFLAARALERAANRRGWSVTTDTRGPDGKTDNKPSEAAIQQADLV 60

Query: 60 IIAADRSVNKDRFIGKKLLSVGVQDGIRKPEELIQKA 96
          I A    VN D + GK+LL + V   +  P+ ++ +A
Sbjct: 61 IAAVGIPVNLDVYAGKRLLQIPVTAALPDPDAILTRA 97


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: 884
Number of extensions: 58
Number of successful extensions: 9
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: 587
Length adjustment: 37
Effective length of query: 613
Effective length of database: 550
Effective search space:   337150
Effective search space used:   337150
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 preprint 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