GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocA in Algiphilus aromaticivorans DG1253

Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; L-glutamate gamma-semialdehyde dehydrogenase; EC 1.2.1.88 (characterized)
to candidate WP_043769867.1 U743_RS16355 aldehyde dehydrogenase family protein

Query= SwissProt::P94391
         (515 letters)



>NCBI__GCF_000733765.1:WP_043769867.1
          Length = 494

 Score =  238 bits (608), Expect = 3e-67
 Identities = 156/479 (32%), Positives = 239/479 (49%), Gaps = 17/479 (3%)

Query: 41  INGE-RVETEAKIVSINPADKEEVVGRVSKASQEHAEQAIQAAAKAFEE--WRYTSPEER 97
           I GE R E+ A+ +++     E V+G +  +S    ++A++AA KAF +  W   +P ER
Sbjct: 20  IAGEWRDESGAERITVTDPASETVLGDIPCSSAATVDKAVRAARKAFNDPAWSNLAPMER 79

Query: 98  AAVLFRAAAKVRRRKHEFSALLVKEAGKPWN-EADADTAEAIDFMEYYARQMIELAKGKP 156
            A+L R AA V +   + + +   + GKP    +  D   +  ++ Y+A    +L+    
Sbjct: 80  EALLHRLAALVEQHADDLATIESLDNGKPIAFSSTLDVPLSAQWLHYFAGWPSKLSGRSM 139

Query: 157 VNSREGEKNQYVYT---PTGVTVVIPPWNFLFAIMAGTTVAPIVTGNTVVLKPASATPVI 213
             + +   + + YT   P GV   I PWNF   +        +  GNTVV+KPA  TP  
Sbjct: 140 HPAVQPTGSHHAYTLRQPVGVVGAIVPWNFPLVLAIWKLAPALAAGNTVVIKPAEQTPYS 199

Query: 214 AAKFVEVLEESGLPKGVVNFVPGSGAEVGDYLVDHPKTSLITFTGSREVGTRIFERAAKV 273
             K  E++E +G P GVVN V G G   G  +VDHP    I+FTGS  VG  +   AA  
Sbjct: 200 LLKLAELIEAAGFPPGVVNVVLGDGRTTGQAIVDHPGVDKISFTGSTAVGKHLLTSAA-- 257

Query: 274 QPGQQHLKRVIAEMGGKDTVVVDEDADIELAAQSIFTSAFGFAGQKCSAGSRAVVHEKVY 333
                 LKRV  E+GGK   V+  DAD+E A      + F  +GQ C AG+R     K +
Sbjct: 258 ----NDLKRVTLELGGKSPTVILPDADLETAIPGAAQAVFVNSGQICFAGTRLFAPRKHF 313

Query: 334 DQVLERVIEITESKVTAKPDSADVYMGPVIDQGSYDKIMSYIEIGKQEG-RLVSGGTGDD 392
           D++LE V E  +S         +  +GPV+ Q   D I+  +E G + G     GG   D
Sbjct: 314 DRILEGVAEAAKSFPVGAGLDPNSMLGPVVSQQQMDSILGKVEAGVKAGASTFCGGGRLD 373

Query: 393 SKGYFIKPTIFADLDPKARLMQEEIFGPVVAFCKVSDFDEALEVANNTEYGLTGAVITNN 452
            +GYF++PTI    D +    +EEIFGPV+   +  + D+ + +AN++EYGL+  + T++
Sbjct: 374 REGYFLEPTILVTDDAQNPAYREEIFGPVLTATRYDELDDIIAMANDSEYGLSANLYTSH 433

Query: 453 RKHIERAKQEFHVGNLYFNRNCTGAIVGYHPFGGFKMSGTDSKAGGPDYLALHMQAKTI 511
                R   +   G ++ N   +     + PFGGFK SG   +  G D  A + + K++
Sbjct: 434 FGLAHRLAAQLQAGTVWINTQLSPD--PHIPFGGFKQSGW-GRENGEDVFAHYTETKSV 489


Lambda     K      H
   0.316    0.133    0.379 

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: 584
Number of extensions: 31
Number of successful extensions: 4
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: 494
Length adjustment: 34
Effective length of query: 481
Effective length of database: 460
Effective search space:   221260
Effective search space used:   221260
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 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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