GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Pseudomonas stutzeri RCH2

Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate GFF2388 Psest_2436 methylmalonic acid semialdehyde dehydrogenase

Query= BRENDA::Q9EQ20
         (535 letters)



>FitnessBrowser__psRCH2:GFF2388
          Length = 503

 Score =  616 bits (1589), Expect = 0.0
 Identities = 296/488 (60%), Positives = 373/488 (76%)

Query: 33  SSSSVPTVKLFIDGKFVESKSDKWIDIHNPATNEVVGRVPQSTKAEMDAAVESCKRAFPA 92
           +SSS+PTVKL IDG+F+ES +  W D+ NPAT EV+ RVP +T  E+D AV S ++AF  
Sbjct: 3   TSSSIPTVKLLIDGEFIESTTQDWRDVVNPATQEVLARVPFATAEEIDRAVASGQKAFKT 62

Query: 93  WADTSILSRQQVLLRYQQLIKENLKEIARLITLEQGKTLADAEGDVFRGLQVVEHACSVT 152
           W  T I +R ++ L+YQQLI+EN+KE+A ++T EQGKTLADAEGDVFRGL+VVEHA  + 
Sbjct: 63  WRKTPIGARARIFLKYQQLIRENMKELAAILTAEQGKTLADAEGDVFRGLEVVEHAAGIG 122

Query: 153 SLMLGETMPSITKDMDLYSYRLPLGVCAGIAPFNFPAMIPLWMFPMAMVCGNTFLMKPSE 212
           +L LGE   ++   +D Y+   PLGVCAGI PFNFPAMIPLWMFPMA+  GNTF++KPSE
Sbjct: 123 NLQLGELANNVAAGVDTYTLLQPLGVCAGITPFNFPAMIPLWMFPMAIATGNTFVLKPSE 182

Query: 213 RVPGATMLLAKLLQDSGAPDGTLNIIHGQHDAVNFICDHPDIKAISFVGSNQAGEYIFER 272
           + P  TM L +L  ++G P G LN++HG  D VN ICDHPDIKA+SFVGS + G +++ R
Sbjct: 183 QDPMVTMRLCELALEAGVPPGVLNVVHGGPDVVNAICDHPDIKAVSFVGSTKVGTHVYNR 242

Query: 273 GSRNGKRVQANMGAKNHGVVMPDANKENTLNQLVGAAFGAAGQRCMALSTAILVGEAKKW 332
            S+ GKRVQ  MGAKNH +V+PDA+KE TLN L GAAFGAAGQRCMALS  +LVGEA+ W
Sbjct: 243 ASQAGKRVQCMMGAKNHAIVLPDAHKEQTLNNLAGAAFGAAGQRCMALSVVVLVGEAQAW 302

Query: 333 LPELVDRAKNLRVNAGDQPGADLGPLITPQAKERVCNLIDSGTKEGASILLDGRRIKVKG 392
           +P+LV +A+ L+VNAG + G D+GPL++  A +RV  LI+ G +EGA + LDGR   V G
Sbjct: 303 IPDLVAKAQTLKVNAGVEAGTDVGPLVSCAALDRVSGLIERGVREGAKLELDGRNPSVSG 362

Query: 393 YENGNFVGPTIISNVKPSMTCYKEEIFGPVLVVLETETLDEAIKIVNDNPYGNGTAIFTT 452
           YENGNFVGPTI S V   M+ Y+EEIFGPVL V+   T+DEAI+++N NP GNGTAIFT 
Sbjct: 363 YENGNFVGPTIFSGVTREMSVYQEEIFGPVLCVMAAATMDEAIELINANPNGNGTAIFTR 422

Query: 453 NGATARKYAHMVDVGQVGVNVPIPVPLPMFSFTGSRSSFRGDTNFYGKQGIQFYTQLKTI 512
           +GA AR +   +DVGQVG+NVPIPVP+PMFSFTGSR+S  GD   YGKQ +QFYTQ KTI
Sbjct: 423 SGAAARHFQEEIDVGQVGINVPIPVPVPMFSFTGSRASKLGDLGPYGKQVVQFYTQTKTI 482

Query: 513 TSQWKEED 520
           T +W +E+
Sbjct: 483 TERWFDEN 490


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: 695
Number of extensions: 27
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: 503
Length adjustment: 35
Effective length of query: 500
Effective length of database: 468
Effective search space:   234000
Effective search space used:   234000
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