GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocA 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)



>FitnessBrowser__Pedo557:CA265_RS14635
          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:

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