GapMind for catabolism of small carbon sources

 

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

Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate H281DRAFT_01202 H281DRAFT_01202 methylmalonate-semialdehyde dehydrogenase [acylating]

Query= BRENDA::Q02252
         (535 letters)



>FitnessBrowser__Burk376:H281DRAFT_01202
          Length = 502

 Score =  603 bits (1554), Expect = e-177
 Identities = 280/482 (58%), Positives = 366/482 (75%)

Query: 39  TVKLFIGGKFVESKSDKWIDIHNPATNEVIGRVPQATKAEMDAAIASCKRAFPAWADTSV 98
           TVKL I G+FV+S++ +W D+ NPAT +V+ RVP AT  E+D AI S   AF  W DT +
Sbjct: 8   TVKLLINGEFVDSRTTEWRDVVNPATQQVLARVPFATAGEVDEAIRSAHAAFKTWKDTPI 67

Query: 99  LSRQQVLLRYQQLIKENLKEIAKLITLEQGKTLADAEGDVFRGLQVVEHACSVTSLMMGE 158
            +R +++L+YQ LI+E++  IAK ++ EQGKT+ DAEGD+FRGL+VVEHACS+ SL  GE
Sbjct: 68  GARMRIMLKYQALIREHMPRIAKTLSAEQGKTIPDAEGDIFRGLEVVEHACSIGSLQQGE 127

Query: 159 TMPSITKDMDLYSYRLPLGVCAGIAPFNFPAMIPLWMFPMAMVCGNTFLMKPSERVPGAT 218
              ++   +D Y+ R PLGVCAGI PFNFPAMIPLWMFPMA+VCGNTF++KPSE+ P +T
Sbjct: 128 FAENVAGGVDTYTLRQPLGVCAGITPFNFPAMIPLWMFPMAIVCGNTFVLKPSEQDPMST 187

Query: 219 MLLAKLLQDSGAPDGTLNIIHGQHEAVNFICDHPDIKAISFVGSNKAGEYIFERGSRHGK 278
           M L +L  ++G P G LN++HG  + V+ +C H  +KA+SFVGS   G +++  GS HGK
Sbjct: 188 MQLVELALEAGVPKGVLNVVHGGKDVVDALCTHELVKAVSFVGSTAVGTHVYRLGSEHGK 247

Query: 279 RVQANMGAKNHGVVMPDANKENTLNQLVGAAFGAAGQRCMALSTAVLVGEAKKWLPELVE 338
           RVQ+ MGAKNH VV+PDAN+E TLN L GA FGAAGQRCMA S  VLVG A++WLPE+V 
Sbjct: 248 RVQSMMGAKNHAVVLPDANREQTLNALAGAGFGAAGQRCMATSVVVLVGAAQQWLPEIVA 307

Query: 339 HAKNLRVNAGDQPGADLGPLITPQAKERVCNLIDSGTKEGASILLDGRKIKVKGYENGNF 398
            AK L+VNAG++P  D+GP+++  AKER+  LI++G KEGA++ LDGR + V GYE GNF
Sbjct: 308 KAKTLKVNAGNEPNTDIGPVVSRAAKERILGLIEAGVKEGATLALDGRDVTVPGYEQGNF 367

Query: 399 VGPTIISNVKPNMTCYKEEIFGPVLVVLETETLDEAIQIVNNNPYGNGTAIFTTNGATAR 458
           +GPTI S+V   M  Y+ EIFGPVL+VL   TLD+AI +VN+NP+GNG  +FT +GA AR
Sbjct: 368 IGPTIFSDVSTEMEIYRTEIFGPVLLVLNAATLDDAIALVNSNPFGNGVGLFTQSGAAAR 427

Query: 459 KYAHLVDVGQVGVNVPIPVPLPMFSFTGSRSSFRGDTNFYGKQGIQFYTQLKTITSQWKE 518
           K+   +DVGQVG+N+PIPVP+P FSFTGSR S  GD   YGKQ +QFYTQ KT+T++W +
Sbjct: 428 KFQSEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQFYTQTKTVTARWFD 487

Query: 519 ED 520
           +D
Sbjct: 488 DD 489


Lambda     K      H
   0.318    0.133    0.391 

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: 678
Number of extensions: 28
Number of successful extensions: 1
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: 535
Length of database: 502
Length adjustment: 35
Effective length of query: 500
Effective length of database: 467
Effective search space:   233500
Effective search space used:   233500
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