GapMind for catabolism of small carbon sources

 

Aligments for a candidate for praB in Pseudomonas fluorescens FW300-N2E3

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate AO353_07805 AO353_07805 betaine-aldehyde dehydrogenase

Query= metacyc::MONOMER-15108
         (486 letters)



>lcl|FitnessBrowser__pseudo3_N2E3:AO353_07805 AO353_07805
           betaine-aldehyde dehydrogenase
          Length = 490

 Score =  379 bits (972), Expect = e-109
 Identities = 202/476 (42%), Positives = 292/476 (61%), Gaps = 5/476 (1%)

Query: 14  FIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANER 73
           +IDG +  +    TF+ INPA  E L TV     A+++ AV +A+K     W  MTA ER
Sbjct: 10  YIDGGYSDASGDATFEAINPANGEVLATVQRATFADVERAVVSAEKGQK-IWAAMTAMER 68

Query: 74  IAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEAT 133
             +LR+  +++ ER +EL+ LE+LDTGK    +  +DI   A    +++  +  I  E  
Sbjct: 69  SRILRRAVEILRERNDELAALETLDTGKAYSETRYVDIVTGADVLEYYAGLVPAIEGEQI 128

Query: 134 QMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATVL 193
            +   +  Y  R P+G++  I  WN P+ +  WK APALAAGN ++ KP+E+T +T   L
Sbjct: 129 PLRTTSFVYTRREPLGIVAGIGAWNYPIQIALWKSAPALAAGNAMIFKPSEVTSLTTLKL 188

Query: 194 AEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAA-KTLK 252
           AEI  +AG+P GV N++ G G    G  LTEHP +  ISFTG T TGK +MASA+  +LK
Sbjct: 189 AEIYTEAGLPAGVFNVLTGSG-REVGTWLTEHPRIEKISFTGGTDTGKKVMASASGSSLK 247

Query: 253 RLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEKFV 312
            ++ ELGGK+P +IF D++LD   +T M ++F + G+VC  G+R++V      AF  K V
Sbjct: 248 DVTMELGGKSPLIIFDDADLDRAADTAMMANFYSSGQVCTNGTRVFVPSHLKAAFEAKIV 307

Query: 313 AKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKR-PEG-LEKGY 370
            +   + VG+P D  T  G L+S  H E V GYI    EEG  +L GG+R  EG   KG 
Sbjct: 308 ERVARIRVGNPEDENTNFGPLVSFAHMESVLGYIAKGKEEGARLLCGGERLTEGEFAKGA 367

Query: 371 FLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLRRA 430
           F+ PT+ T  T +  +V+EEIFGPV++++ ++TEEEV+ + NDT +GL+A V T DL RA
Sbjct: 368 FVAPTVFTDCTDEMTIVREEIFGPVMSILTYETEEEVIRRANDTEFGLAAGVVTRDLNRA 427

Query: 431 HRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNICIKL 486
           HRV  Q+EAGI W+N W   D + P GG KQSG+GRE G+ S   ++ + ++ ++L
Sbjct: 428 HRVIHQLEAGICWINAWGESDAKMPVGGYKQSGVGRENGISSLNNFTRIKSVQVEL 483


Lambda     K      H
   0.318    0.136    0.404 

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: 643
Number of extensions: 27
Number of successful extensions: 5
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: 486
Length of database: 490
Length adjustment: 34
Effective length of query: 452
Effective length of database: 456
Effective search space:   206112
Effective search space used:   206112
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 (21.7 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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