GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praB in Pseudomonas fluorescens FW300-N2C3

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate AO356_13795 AO356_13795 betaine-aldehyde dehydrogenase

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



>FitnessBrowser__pseudo5_N2C3_1:AO356_13795
          Length = 490

 Score =  374 bits (959), Expect = e-108
 Identities = 199/476 (41%), Positives = 288/476 (60%), Gaps = 5/476 (1%)

Query: 14  FIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANER 73
           +IDG +  +    TF+ INPA  E L  V      +++ AV +A+K     W  MTA +R
Sbjct: 10  YIDGAYSDASGDATFEAINPANGEVLALVQRATFEDVERAVVSAEKGQK-VWAAMTAMQR 68

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

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

Query: 194 AEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKT-LK 252
           AEI  +AGVP GV N++ G G    G  LTEHP +  +SFTG T TGK +MASA+ + LK
Sbjct: 189 AEIYTEAGVPAGVFNVLTGSG-REVGTWLTEHPRIEKVSFTGGTDTGKKVMASASSSSLK 247

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

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

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

Query: 431 HRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNICIKL 486
           HR+  Q+EAGI W+N W   D + P GG KQSG+GRE G+ S   ++ + ++ ++L
Sbjct: 428 HRIIHQLEAGICWINAWGESDAKMPVGGYKQSGVGRENGISSLNNFTRIKSVQVEL 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: 635
Number of extensions: 25
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.

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