GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praB in Paraburkholderia bryophila 376MFSha3.1

Align 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized)
to candidate H281DRAFT_03256 H281DRAFT_03256 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase

Query= SwissProt::Q9H2A2
         (487 letters)



>FitnessBrowser__Burk376:H281DRAFT_03256
          Length = 485

 Score =  406 bits (1044), Expect = e-118
 Identities = 207/486 (42%), Positives = 306/486 (62%), Gaps = 21/486 (4%)

Query: 8   LMLENFIDGKFLPCSSYIDSYDPSTGEVYCRVPNSGKDEIEAAVKAAREAFPSWSSRSPQ 67
           + +E+ I+GK      Y ++ +P+T EV   V    + E++AAV+AA+EAFP+W+ +   
Sbjct: 1   MRIEHLINGKAGGAKDYFETVNPATQEVLAEVARGTEAEVDAAVRAAKEAFPAWAGKPAA 60

Query: 68  ERSRVLNQVADLLEQSLEEFAQAESKDQGKTLALARTMDIPRSVQNFRFFASSSLHHTSE 127
           ER++++ ++ +L+ +++ E ++ E+KD G+T++  R   +PR+  NF +FA         
Sbjct: 61  ERAKLIRKLGELIAKNVPEISETETKDTGQTISQTRKQLVPRAADNFSYFAEM------- 113

Query: 128 CTQMD--------HLGCMHYTVRAPVGVAGLISPWNLPLYLLTWKIAPAMAAGNTVIAKP 179
           CT++D        HL   +YT+  PVGV  LISPWN+P    TWK+AP +A GNT + K 
Sbjct: 114 CTRVDGHTYPTDTHL---NYTLFHPVGVCALISPWNVPFMTATWKVAPCLAFGNTAVLKM 170

Query: 180 SELTSVTAWMLCKLLDKAGVPPGVVNIVFGTGPRVGEALVSHPEVPLISFTGSQPTAERI 239
           SEL+ +TA ML  L  +AG+P GV+N+V G G   GE LV+HP+V  +SFTGS  T  RI
Sbjct: 171 SELSPLTASMLGNLALEAGIPAGVLNVVHGFGKETGEPLVAHPDVHAVSFTGSTATGNRI 230

Query: 240 TQLSAPHCKKLSLELGGKNPAIIFEDANLDECIPATVRSSFANQGEICLCTSRIFVQKSI 299
            Q +    KK S+ELGGK+P +IF+DA+ +  + A V   F+N GE C   SRI VQKSI
Sbjct: 231 VQSAG--LKKYSMELGGKSPFVIFDDADFERALDAAVFMIFSNNGERCTAGSRILVQKSI 288

Query: 300 YSEFLKRFVEATRKWKVGIPSDPLVSIGALISKAHLEKVRSYVKRALAEGAQIWCGEGVD 359
           Y++F +RF+E  ++  VG P      IG +IS+ HL KVRSY++    EGA + CG G+D
Sbjct: 289 YAKFAERFIERAKRLTVGDPLADSTIIGPMISQGHLAKVRSYIELGPKEGATLACG-GLD 347

Query: 360 KLSLPARNQAGYFMLPTVITDIKDESCCMTEEIFGPVTCVVPFDSEEEVIERANNVKYGL 419
              LP   + G F++PTV  D+ +      EEIFGPV C++PFD E + I  AN++ YGL
Sbjct: 348 MPGLPDSMRHGNFVMPTVFVDVDNRMRIAQEEIFGPVACLIPFDDEADAIRLANDISYGL 407

Query: 420 AATVWSSNVGRVHRVAKKLQSGLVWTNCWLIRELNLPFGGMKSSGIGREGAKDSYDFFTE 479
           ++ +W+ N GR HRVA  +++G+ + N   +R+L  PFGG K+SG+GREG   SY+ F E
Sbjct: 408 SSYIWTENTGRAHRVAASVEAGMCFVNSQNVRDLRQPFGGTKASGVGREGGTWSYEVFLE 467

Query: 480 IKTITV 485
            K + V
Sbjct: 468 PKNVCV 473


Lambda     K      H
   0.319    0.133    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: 596
Number of extensions: 15
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: 487
Length of database: 485
Length adjustment: 34
Effective length of query: 453
Effective length of database: 451
Effective search space:   204303
Effective search space used:   204303
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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