GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Pseudomonas fluorescens FW300-N1B4

Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate Pf1N1B4_1229 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27)

Query= BRENDA::Q02252
         (535 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1229
          Length = 505

 Score =  608 bits (1568), Expect = e-178
 Identities = 288/491 (58%), Positives = 377/491 (76%)

Query: 31  SSFSSSVPTVKLFIGGKFVESKSDKWIDIHNPATNEVIGRVPQATKAEMDAAIASCKRAF 90
           +S  ++V  VKL I G++VES++ +W DI NPAT +V+ +VP AT AE+DAAI++  RAF
Sbjct: 3   ASLETTVQKVKLLIDGEWVESQTTEWHDIVNPATQQVLAKVPFATAAEVDAAISAAHRAF 62

Query: 91  PAWADTSVLSRQQVLLRYQQLIKENLKEIAKLITLEQGKTLADAEGDVFRGLQVVEHACS 150
             W  T + +R +++L+ Q LI+E+ K IA +++ EQGKT+ADAEGD+FRGL+VVEHACS
Sbjct: 63  QTWKLTPIGARMRIMLKLQALIREHSKRIAVVLSNEQGKTIADAEGDIFRGLEVVEHACS 122

Query: 151 VTSLMMGETMPSITKDMDLYSYRLPLGVCAGIAPFNFPAMIPLWMFPMAMVCGNTFLMKP 210
           + SL MGE   ++   +D Y+ R P+GVCAGI PFNFPAMIPLWMFPMA+ CGNTF++KP
Sbjct: 123 IGSLQMGEFAENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTFVLKP 182

Query: 211 SERVPGATMLLAKLLQDSGAPDGTLNIIHGQHEAVNFICDHPDIKAISFVGSNKAGEYIF 270
           SE+ P +TMLL +L  ++G P G LN++HG  + V+ +C H DIKA+SFVGS   G +++
Sbjct: 183 SEQDPMSTMLLVELAIEAGIPPGVLNVVHGGKDVVDALCTHKDIKAVSFVGSTAVGTHVY 242

Query: 271 ERGSRHGKRVQANMGAKNHGVVMPDANKENTLNQLVGAAFGAAGQRCMALSTAVLVGEAK 330
           +   +HGKRVQ+ MGAKNH VV+PDAN+E  LN LVGA FGAAGQRCMA S  VLVG AK
Sbjct: 243 DLAGKHGKRVQSMMGAKNHAVVLPDANREQALNALVGAGFGAAGQRCMATSVVVLVGAAK 302

Query: 331 KWLPELVEHAKNLRVNAGDQPGADLGPLITPQAKERVCNLIDSGTKEGASILLDGRKIKV 390
           +WLP+L   A+ L+VNAG +PG D+GP+I+ +AK R+ +LI+SG KEGA + LDGR I V
Sbjct: 303 QWLPDLKALAQKLKVNAGSEPGTDVGPVISKRAKARILDLIESGIKEGAKLELDGRDISV 362

Query: 391 KGYENGNFVGPTIISNVKPNMTCYKEEIFGPVLVVLETETLDEAIQIVNNNPYGNGTAIF 450
            GYE GNFVGPT+ S V P M  Y +EIFGPVLVVLE +TLD+AI +VN NP+GNGT +F
Sbjct: 363 PGYEKGNFVGPTLFSGVTPEMQIYTQEIFGPVLVVLEVDTLDQAIALVNANPFGNGTGLF 422

Query: 451 TTNGATARKYAHLVDVGQVGVNVPIPVPLPMFSFTGSRSSFRGDTNFYGKQGIQFYTQLK 510
           T +GA ARK+   +DVGQVG+N+PIPVP+P FSFTGSR S  GD   YGKQ +QFYTQ K
Sbjct: 423 TQSGAAARKFQTEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQFYTQTK 482

Query: 511 TITSQWKEEDA 521
           T+T++W ++D+
Sbjct: 483 TVTARWFDDDS 493


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: 660
Number of extensions: 31
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: 505
Length adjustment: 35
Effective length of query: 500
Effective length of database: 470
Effective search space:   235000
Effective search space used:   235000
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