GapMind for catabolism of small carbon sources

 

Aligments for a candidate for putA in Pedobacter sp. GW460-11-11-14-LB5

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate CA265_RS14635 CA265_RS14635 aldehyde dehydrogenase

Query= BRENDA::Q9K9B2
         (515 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS14635 CA265_RS14635 aldehyde
           dehydrogenase
          Length = 501

 Score =  218 bits (555), Expect = 4e-61
 Identities = 149/429 (34%), Positives = 222/429 (51%), Gaps = 25/429 (5%)

Query: 76  EKAIQSADEAFQTWRNVNPEERANILVKAAAIIRRRKHEFSAWLVHEAGKPWKEA-DADT 134
           E A+ +A EAF+TW   +  ER+ IL K A  +       +A    + GK  +E   AD 
Sbjct: 54  ELAVDAAHEAFKTWSKTSSTERSIILNKIAQRMEDNLEYLAAVETIDNGKAVRETLAADL 113

Query: 135 AEAIDFLEYYARQMIELNRGKEILSRPGEQNRYFYTPMGVTVTISPWNFALAIMVGTAVA 194
              +D   Y+A  +I    G          +   + P+GV   I PWNF L + +     
Sbjct: 114 PLGVDHFRYFAG-VIRAEEGSLSELDQNTVSLIVHEPIGVVAQIIPWNFPLLMGIWKLAP 172

Query: 195 PIVTGNTVVLKPASTTPVVAAKFVEVLEDAGLPKGVINYVPGSGAEVGDYLVDHPKTSLI 254
            +  GN VVLKPA +TPV     +E++ D  LP GV+N V G G+E+G  LV +PK S  
Sbjct: 173 ALAAGNCVVLKPAESTPVSIMVLMELIGDL-LPPGVVNVVNGFGSELGRALVTNPKVSKA 231

Query: 255 TFTGSKDVGVRLYERAAVVRPGQNHLKRVIVEMGGKD------TVVVDRDADLDLAAESI 308
            FTGS   G        V++    ++  V +E+GGK       +V+ + DA LD A E  
Sbjct: 232 AFTGSTPTG------RLVMQYATENIIPVTLELGGKSPNIFFSSVMAEDDAFLDKAVEGA 285

Query: 309 LVSAFGFSGQKCSAGSRAVIHKDVYDEVLEKTVALAKNLTVGDPTNRDNYMGPVIDEKAF 368
           ++ A    G+ C+  SR +I +D+Y++ + K +   K + +G P +R   MG    +  F
Sbjct: 286 VMFALN-QGEICTCPSRLLIQEDIYEKFIAKVIERTKAIKIGSPLDRTVMMGAQASKIQF 344

Query: 369 EKIMSYIEIGKKEG-RLMTGGE-----GDSSTGFFIQPTIIADLDPEAVIMQEEIFGPVV 422
           EKI +YI++GK+EG  ++TGGE     G+   G++I+PTI    + +  I QEEIFGPV+
Sbjct: 345 EKIAAYIKLGKEEGAEVLTGGEINELPGELGGGYYIKPTIFKGHN-KMRIFQEEIFGPVL 403

Query: 423 AFSKANDFDHALEIANNTEYGLTGAVITRNRAHIEQAKREFHVGNLYFNRNCTGAIVGYH 482
           A +     + A+EIAN+T YGL   V TR+   + Q  R    G ++ N+    A     
Sbjct: 404 AVTTFKTVEEAIEIANDTLYGLGAGVWTRDAHELYQVPRAIQAGRVWVNQ--YHAYPAGA 461

Query: 483 PFGGFKMSG 491
           PFGG+K SG
Sbjct: 462 PFGGYKQSG 470


Lambda     K      H
   0.316    0.134    0.388 

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: 592
Number of extensions: 36
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: 515
Length of database: 501
Length adjustment: 34
Effective length of query: 481
Effective length of database: 467
Effective search space:   224627
Effective search space used:   224627
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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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