GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Pedobacter sp. GW460-11-11-14-LB5

Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate CA265_RS14635 CA265_RS14635 aldehyde dehydrogenase

Query= BRENDA::P23883
         (495 letters)



>FitnessBrowser__Pedo557:CA265_RS14635
          Length = 501

 Score =  319 bits (817), Expect = 2e-91
 Identities = 185/483 (38%), Positives = 277/483 (57%), Gaps = 16/483 (3%)

Query: 23  FINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAK 82
           +I G++ A  +   F+ + P+      K A     D++ A+ AA   F+   WS +S  +
Sbjct: 17  YIGGKFVAPVKGAYFDNISPIDGKVFTKAAHSTKEDLELAVDAAHEAFKT--WSKTSSTE 74

Query: 83  RKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGEV 142
           R  +LNK+A  ME + E LA +ET+D GK +R +L  D+P      R++A  I    G +
Sbjct: 75  RSIILNKIAQRMEDNLEYLAAVETIDNGKAVRETLAADLPLGVDHFRYFAGVIRAEEGSL 134

Query: 143 ATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAIR 202
           +    + +++IV EP+GV+A I+PWNFPLL+  WKL PALAAGN V+LKP+E +P+S + 
Sbjct: 135 SELDQNTVSLIVHEPIGVVAQIIPWNFPLLMGIWKLAPALAAGNCVVLKPAESTPVSIMV 194

Query: 203 LAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNMK 262
           L  L  +  LP GV+NVV GFG E G+AL  +  +   AFTGST TG+ +++ A + N+ 
Sbjct: 195 LMELIGDL-LPPGVVNVVNGFGSELGRALVTNPKVSKAAFTGSTPTGRLVMQYATE-NII 252

Query: 263 RVWLEAGGKSANIVF----ADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEF 318
            V LE GGKS NI F    A+       A   A     NQG++C   +RLL++E I ++F
Sbjct: 253 PVTLELGGKSPNIFFSSVMAEDDAFLDKAVEGAVMFALNQGEICTCPSRLLIQEDIYEKF 312

Query: 319 LALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDG-------R 371
           +A + ++ +  + G PLD    MG        + + ++I+ G+ +G  +L G        
Sbjct: 313 IAKVIERTKAIKIGSPLDRTVMMGAQASKIQFEKIAAYIKLGKEEGAEVLTGGEINELPG 372

Query: 372 NAGLAAAIGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWT 431
             G    I PTIF   +    + +EEIFGPVL VT F + E+A+++AND+ YGLGA VWT
Sbjct: 373 ELGGGYYIKPTIFKGHN-KMRIFQEEIFGPVLAVTTFKTVEEAIEIANDTLYGLGAGVWT 431

Query: 432 RDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWI 491
           RD    +++ R ++AG V+VN Y+      PFGGYKQSG GR+     L  + + K + I
Sbjct: 432 RDAHELYQVPRAIQAGRVWVNQYHAYPAGAPFGGYKQSGVGRENHKMMLGHYRQTKNMLI 491

Query: 492 SLE 494
           S +
Sbjct: 492 SYD 494


Lambda     K      H
   0.317    0.133    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: 521
Number of extensions: 18
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: 495
Length of database: 501
Length adjustment: 34
Effective length of query: 461
Effective length of database: 467
Effective search space:   215287
Effective search space used:   215287
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 (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