GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Acidovorax sp. GW101-3H11

Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate Ac3H11_2357 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27)

Query= BRENDA::Q02252
         (535 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2357
          Length = 507

 Score =  612 bits (1578), Expect = e-179
 Identities = 297/487 (60%), Positives = 374/487 (76%), Gaps = 1/487 (0%)

Query: 38  PTVKLFIGGKFVESKSDKWIDIHNPATNEVIGRVPQATKAEMDAAIASCKRAFPAWADTS 97
           PTVKL IGGKFVESK+ +W D+ NPAT EV+ RVP AT  E+DAA+AS + AF  W  T+
Sbjct: 12  PTVKLLIGGKFVESKTTQWRDVVNPATQEVLARVPFATPEEIDAAVASAQEAFKTWKKTA 71

Query: 98  VLSRQQVLLRYQQLIKENLKEIAKLITLEQGKTLADAEGDVFRGLQVVEHACSVTSLMMG 157
           + +R ++ L+YQQLI+EN+ E+A ++T EQGKTL DAEGDVFRGL+VVEHA S+ +L +G
Sbjct: 72  IGARARIFLKYQQLIRENMAELAAILTAEQGKTLPDAEGDVFRGLEVVEHAASIGNLQLG 131

Query: 158 ETMPSITKDMDLYSYRLPLGVCAGIAPFNFPAMIPLWMFPMAMVCGNTFLMKPSERVPGA 217
           E   ++   +D Y+   PLGVCAGI PFNFPAMIPLWMFPMA+  GNTF++KPSE+ P  
Sbjct: 132 ELANNVAGGVDTYTLMQPLGVCAGITPFNFPAMIPLWMFPMAIATGNTFVLKPSEQDPMV 191

Query: 218 TMLLAKLLQDSGAPDGTLNIIHGQHEAVNFICDHPDIKAISFVGSNKAGEYIFERGSRHG 277
           TM L +L  ++G P G LN+IHG   AVN ICDH DIKAISFVGS K G +++ R S +G
Sbjct: 192 TMRLVELALEAGIPPGVLNVIHGGEAAVNAICDHKDIKAISFVGSTKVGTHVYNRASLNG 251

Query: 278 KRVQANMGAKNHGVVMPDANKENTLNQLVGAAFGAAGQRCMALSTAVLVGEAKKWLPELV 337
           KRVQ  MGAKNH +VMPDANKE TLN L GAAFGAAGQRCMALS  VLVGEA+KW+PELV
Sbjct: 252 KRVQCMMGAKNHAIVMPDANKEQTLNALAGAAFGAAGQRCMALSVVVLVGEAQKWIPELV 311

Query: 338 EHAKNLRVNAGDQPGADLGPLITPQAKERVCNLIDSGTKEGASILLDGRKIKVKGYENGN 397
             AK L+V+AG + G D+GP+++  AK+RV +LI+ G  +GA++ LDGR  +V GYE GN
Sbjct: 312 AKAKTLKVSAGVEKGTDVGPVVSCAAKDRVQSLIERGIADGATLELDGRNPEVAGYEKGN 371

Query: 398 FVGPTIISNVKPNMTCYKEEIFGPVLVVLETETLDEAIQIVNNNPYGNGTAIFTTNGATA 457
           FVGPT+ S VKP M+ Y +EIFGPVL +     +DEAI  +N+NP GNGTAIFT +GA A
Sbjct: 372 FVGPTVFSGVKPGMSIYDQEIFGPVLCLSAAADIDEAIAFINDNPNGNGTAIFTQSGAAA 431

Query: 458 RKYAHLVDVGQVGVNVPIPVPLPMFSFTGSRSSFRGDTNFYGKQGIQFYTQLKTITSQWK 517
           RK+   +DVGQVG+NVPIPVP+P+FSF+GSR+S  GD   YGKQ + FYTQ KT+T++W 
Sbjct: 432 RKFQEEIDVGQVGINVPIPVPVPLFSFSGSRASKLGDLGPYGKQVVLFYTQTKTVTARW- 490

Query: 518 EEDATLS 524
            +D+T+S
Sbjct: 491 FDDSTIS 497


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: 709
Number of extensions: 33
Number of successful extensions: 2
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: 507
Length adjustment: 35
Effective length of query: 500
Effective length of database: 472
Effective search space:   236000
Effective search space used:   236000
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