Aligments for a candidate for puuA in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Aligments for a candidate for puuA in Phaeobacter inhibens BS107

Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate GFF1137 PGA1_c11520 gamma-glutamylputrescine synthetase PuuA

Query= reanno::BFirm:BPHYT_RS23160
         (444 letters)



>FitnessBrowser__Phaeo:GFF1137
          Length = 452

 Score =  461 bits (1186), Expect = e-134
 Identities = 221/438 (50%), Positives = 290/438 (66%)

Query: 7   FLKKNRVTEIEAIIPDMAGIARGKIIPRSKFESGESMRLPQAVMIQTVTGDYPEDGTLTG 66
           +L+  R+ E+E II D+ GIARGK +P SKF   +   LP ++  QT+TGD+ E     G
Sbjct: 15  YLEGRRLDEVECIISDLPGIARGKAVPASKFAKQDYFHLPDSIFYQTITGDWAEAADDDG 74

Query: 67  VTDPDMVCVPDASTIRMIPWAVDPTAQVIHDCVHFDGTPVAISPRRVLRRVLELYKAKGW 126
             + DM+  PD ST    PW  D T QVIHD    D  P+  SPR VL+RV++LY  KGW
Sbjct: 75  WIEKDMILKPDMSTATAAPWTGDWTLQVIHDAYDRDHKPIPFSPRNVLKRVVQLYHDKGW 134

Query: 127 KPVIAPELEFYLVDMNKDPDLPLQPPIGRTGRPETGRQAYSIEAVNEFDPLFEDIYEYCE 186
           +PV+APE+EF+LV  N DP   ++P +GR+GRP   RQAYS+ AV+EF P+ +DIY++ E
Sbjct: 135 QPVVAPEMEFFLVARNIDPAREIEPMMGRSGRPAAARQAYSMTAVDEFGPVIDDIYDFAE 194

Query: 187 VQELEVDTLIHEVGAAQMEINFMHGDPLKLADSVFLFKRTVREAALRHKMYATFMAKPME 246
            Q  E+D +  E GA Q+EIN  HGDP+KLAD VF FKR +REAALRH  +ATFMAKP+ 
Sbjct: 195 AQGFEIDGITQEGGAGQLEINLRHGDPVKLADEVFYFKRLIREAALRHDCFATFMAKPIA 254

Query: 247 GEPGSAMHMHQSLVDEETGHNLFTGPDGKPTSLFTSYIAGLQKYTPALMPIFAPYINSYR 306
            EPGSAMH+H S++D E+G N+F+GP G  T  F  +I GLQ + PA + + APY+NSYR
Sbjct: 255 DEPGSAMHIHHSIIDMESGDNIFSGPQGGETDAFYHFIGGLQNHLPAGLAVMAPYVNSYR 314

Query: 307 RLSRFMAAPINVAWGYDNRTVGFRIPHSGPAARRIENRIPGVDCNPYLAIAATLAAGYLG 366
           R  +  AAPIN+ W  DNRT G R+P SGP ARR+ENRI G+DCNPYL IA +LA GYLG
Sbjct: 315 RYVKEQAAPINLEWARDNRTTGIRVPLSGPEARRVENRIAGMDCNPYLGIALSLACGYLG 374

Query: 367 MTQKLEATEPLLSDGYELPYQLPRNLEEGLTLMGACEPIAEVLGEKFVKAYLALKETEYE 426
           +  +    +    D Y     +P+ + + L L      + EVLG +F + Y  +K  EY+
Sbjct: 375 LVNEERPRKQFKGDAYAGDGDIPQVMGQALDLFEEASALHEVLGPEFARVYSIVKRAEYD 434

Query: 427 AFFRVISSWERRHLLLHV 444
            F +VIS WER HLLL+V
Sbjct: 435 EFLQVISPWEREHLLLNV 452


Lambda     K      H
   0.321    0.138    0.418 

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: 632
Number of extensions: 19
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: 444
Length of database: 452
Length adjustment: 33
Effective length of query: 411
Effective length of database: 419
Effective search space:   172209
Effective search space used:   172209
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: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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

GapMind for catabolism of small carbon sources