GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabD in Herbaspirillum seropedicae SmR1

Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate HSERO_RS19755 HSERO_RS19755 betaine-aldehyde dehydrogenase

Query= BRENDA::P23883
         (495 letters)



>FitnessBrowser__HerbieS:HSERO_RS19755
          Length = 484

 Score =  353 bits (905), Expect = e-101
 Identities = 196/477 (41%), Positives = 286/477 (59%), Gaps = 8/477 (1%)

Query: 23  FINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAK 82
           FI GE T A++ +    V+P+ +   A  A+G + D+ RA++AA+   E G WS  S  +
Sbjct: 8   FIAGEATEASDGQRMNLVNPINEEIYASAAQGTAADVARAVAAAKAQLEGGAWSKLSGLQ 67

Query: 83  RKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGEV 142
           R  +L+KLA L+E   + LA ++    G+        D+P A   +R  A   +++ G  
Sbjct: 68  RGQLLHKLAALVERDTDLLADMDARAIGRSPMEPRMMDVPNAISHLRAAAGWANQMEGRT 127

Query: 143 ATTSSH----ELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPL 198
             T+ +     L+  VREP+GV+ AI+PWN PL++T WK+   LAAG +V++KP+E++P 
Sbjct: 128 IPTAGYMGKPTLSYTVREPIGVVGAILPWNAPLMITSWKVAALLAAGCTVVIKPAEETPQ 187

Query: 199 SAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGD 258
           SA+ LA LA+EAG PDGV+NVVTG+G+  G+AL  H D+  I+FTGS   G+ + + AG+
Sbjct: 188 SALHLARLAQEAGFPDGVINVVTGYGNSVGRALCEHPDVAKISFTGSPEAGRAIQRIAGE 247

Query: 259 SNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEF 318
              KRV LE GGKS  IVF D P  + A      G+F NQGQVC AG+R+L++ S+A  F
Sbjct: 248 -QFKRVTLELGGKSPQIVFDDAP-FEDALFGCTLGLFVNQGQVCAAGSRILVQRSLAQRF 305

Query: 319 LALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDG--RNAGLA 376
              L + A     G P  P   MG +   A  + V+ +I++G  +G  LL G        
Sbjct: 306 AKALAEAAAGITVGDPSQPGVRMGPVAKKAQFERVNRYIQQGLDEGATLLAGGVSRPDKG 365

Query: 377 AAIGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRDLSR 436
             + PTIF D +   S++REEIFGPV  +  F +EE+A+ LANDS+YGL A VWT +L+R
Sbjct: 366 WFVQPTIFADANNGMSIAREEIFGPVGTIISFDTEEEAIALANDSKYGLAATVWTTNLAR 425

Query: 437 AHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWISL 493
           AHR++  +K G+V VN ++  D  +P+GG K SG GR+  L     +TE KT+ + L
Sbjct: 426 AHRVAAGVKVGAVGVNCWSPLDANLPWGGIKDSGMGREGGLAGALAYTEEKTVTVLL 482


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: 545
Number of extensions: 18
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: 495
Length of database: 484
Length adjustment: 34
Effective length of query: 461
Effective length of database: 450
Effective search space:   207450
Effective search space used:   207450
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