Aligments for a candidate for kauB in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Aligments for a candidate for kauB in Burkholderia phytofirmans PsJN

Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate BPHYT_RS23175 BPHYT_RS23175 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase

Query= metacyc::MONOMER-11560
         (497 letters)



>FitnessBrowser__BFirm:BPHYT_RS23175
          Length = 497

 Score =  644 bits (1662), Expect = 0.0
 Identities = 318/492 (64%), Positives = 386/492 (78%), Gaps = 3/492 (0%)

Query: 7   ADWEQRAQQLKIEGRAFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENA 66
           A W+ +A  L IEGRAFI+GEY DA  G TF+CLSP+DG+ LAKVA    AD + AV  A
Sbjct: 7   AFWQDKAATLSIEGRAFIDGEYRDAEGGRTFDCLSPIDGKLLAKVADSGAADVDAAVAAA 66

Query: 67  RATFNSGVWSQLAPAKRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQ 126
           R  F+SGVWS L P +RKA L+R+A  +R++++ELALLETLD GKPI D++S+D+PGAA 
Sbjct: 67  RRAFDSGVWSGLNPRQRKAVLLRWAASIREHMDELALLETLDAGKPIADTTSVDVPGAAY 126

Query: 127 AIHWTAEAIDKVYDEVAPTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGN 186
            + W AEAIDK+  EVAP  H  LGLVTREP+GVV A+VPWNFP+LMA WK GPALA GN
Sbjct: 127 CVEWFAEAIDKIGGEVAPADHHLLGLVTREPIGVVAAVVPWNFPILMASWKFGPALAAGN 186

Query: 187 SVVLKPSEKSPLTAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGST 246
           SVVLKPSEKSPLTAIR+AQLA++AGIPAGV NV+PG G   GK LALH DVD L FTGST
Sbjct: 187 SVVLKPSEKSPLTAIRLAQLALDAGIPAGVFNVVPGAGEP-GKLLALHQDVDCLAFTGST 245

Query: 247 KIAKQLMVYAGESNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGS 306
            + K +M YAG+SN+KR+WLE GGKSPNIV  D PD+  AA AAA AI +N GE+CTAGS
Sbjct: 246 NVGKLIMQYAGQSNLKRVWLELGGKSPNIVMPDCPDMDRAANAAAGAIFYNMGEMCTAGS 305

Query: 307 RLLVERSIKDKFLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAK 366
           RLLV R IKD F+  ++ A + + PGNPLDP T++GA+VD  Q+  VL YIEAG  + AK
Sbjct: 306 RLLVHRDIKDVFIDKLIAAARSYTPGNPLDPDTSMGAIVDKVQLERVLGYIEAGRAE-AK 364

Query: 367 LLAGGKRTLEETGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTP 426
           LL GG R  E+TGG Y+EPTIF+   +  ++A+EEIFGPVLSVI FDT EEA+ IAND+ 
Sbjct: 365 LLLGGARVKEDTGGFYIEPTIFEIPGSGAKVAREEIFGPVLSVITFDTVEEAIRIANDSE 424

Query: 427 YGLAAGIWTSDISKAHKTARAVRAGSVWVNQYD-GGDMTAPFGGFKQSGNGRDKSLHALE 485
           YGLAA +WTS+++ AH+ +R +RAG+VWVN YD GGDM  PFGG+KQSGNGRDKSLHALE
Sbjct: 425 YGLAAAVWTSNLTTAHEVSRKLRAGTVWVNCYDEGGDMNFPFGGYKQSGNGRDKSLHALE 484

Query: 486 KYTELKATWIKL 497
           KYTELK+T ++L
Sbjct: 485 KYTELKSTLVRL 496


Lambda     K      H
   0.316    0.132    0.390 

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: 777
Number of extensions: 29
Number of successful extensions: 6
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: 497
Length of database: 497
Length adjustment: 34
Effective length of query: 463
Effective length of database: 463
Effective search space:   214369
Effective search space used:   214369
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)

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

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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