GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aldA in Pseudomonas fluorescens FW300-N1B4

Align lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate Pf1N1B4_1109 2-ketoglutaric semialdehyde dehydrogenase (EC 1.2.1.26)

Query= BRENDA::Q97UA1
         (478 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1109
          Length = 481

 Score =  353 bits (905), Expect = e-102
 Identities = 194/476 (40%), Positives = 279/476 (58%), Gaps = 10/476 (2%)

Query: 9   DKWIKG---SGEEY-LDINPADKDHVLAKIRLYTKDDVKEAINKAVAKFDEWSRTPAPKR 64
           D +I G   SG +Y  +INP++    +          V  AI+ A A F  WS +    R
Sbjct: 8   DNYINGEWVSGADYSANINPSELTDTIGDYAKADLAQVHAAIDAARAAFPAWSTSGIQAR 67

Query: 65  GSILLKAGELMEQEAQEFALLMTLEEGKTLKDSMFEVTRSYNLLKFYGALAFKISGKTLP 124
              L K G  +    +E   L+  EEGKTL +++ EVTR+ N+ KF+     ++SG  LP
Sbjct: 68  HDSLDKVGTEILARREELGTLLAREEGKTLPEAIGEVTRAGNIFKFFAGECLRLSGDYLP 127

Query: 125 SADPNTRIFTVKEPLGVVALITPWNFPLSIPVWKLAPALAAGNTAVIKPATKTPLMVAKL 184
           S  P   +   +E LGVV LITPWNFP++IP WK+APALA GN  V+KPA   P     L
Sbjct: 128 SVRPGVNVEVTREALGVVGLITPWNFPIAIPAWKIAPALAYGNCVVLKPADLVPGCAWAL 187

Query: 185 VEVLSKAGLPEGVVNLVVGKGSEVGDTIVSDDNIAAVSFTGSTEVGKRIYKLVGNKNRMT 244
            E++S+AG P GV NLV+G G  VGD +V    +  +SFTGS  VG++I   V   +R  
Sbjct: 188 AEIISRAGFPAGVFNLVMGSGRVVGDALVQSPKVDGISFTGSVGVGRQI--AVSCVSRQA 245

Query: 245 RIQLELGGKNALYVDKSADLTLAAELAVRGGFGLTGQSCTATSRLIINKDVYTQFKQRLL 304
           ++QLE+GGKN   +   ADL  A EL+V+  F  TGQ CTA+SR I+   ++ +F + + 
Sbjct: 246 KVQLEMGGKNPQIILDDADLKQAVELSVQSAFYSTGQRCTASSRFIVTAGIHDKFVEAMA 305

Query: 305 ERVKKWRVGPGTE-DVDMGPVVDEGQFKKDLEYIEYGKNVGAKLIYGGNII--PGKGYFL 361
           ER+K  +VG   +   D+GPVV + Q ++DL+YI+ G++ GA+L+ GG ++    +GYFL
Sbjct: 306 ERMKSIKVGHALKTGTDIGPVVSQAQLEQDLKYIDIGQSEGARLVSGGGLVACDTEGYFL 365

Query: 362 EPTIFEGVTSDMRLFKEEIFGPVLSVTEAKDLDEAIRLVNAVDYGHTAGIVASDIKAINE 421
            PT+F   T+ MR+ +EEIFGPV ++    D + A+ + N  ++G +AGI  + +K  N 
Sbjct: 366 APTLFADSTAAMRISREEIFGPVANIVRVADYEAALAMANDTEFGLSAGIATTSLKYANH 425

Query: 422 FVSRVEAGVIKVNKPTVGLELQAPFGGFKNSGATTWKEMGEDALEFYLKEKTVYEG 477
           F    +AG++ VN PT G++   PFGG K S   + +E G  A EFY   KT Y G
Sbjct: 426 FKRHSQAGMVMVNLPTAGVDYHVPFGGRKGSSYGS-REQGRYAQEFYTVVKTSYIG 480


Lambda     K      H
   0.316    0.135    0.389 

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: 553
Number of extensions: 16
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: 478
Length of database: 481
Length adjustment: 34
Effective length of query: 444
Effective length of database: 447
Effective search space:   198468
Effective search space used:   198468
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: 51 (24.3 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