GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Rhizobium freirei PRF 81

Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate WP_004109547.1 RHSP_RS04195 CoA-acylating methylmalonate-semialdehyde dehydrogenase

Query= reanno::Smeli:SMc00781
         (498 letters)



>NCBI__GCF_000359745.1:WP_004109547.1
          Length = 498

 Score =  893 bits (2307), Expect = 0.0
 Identities = 431/498 (86%), Positives = 466/498 (93%)

Query: 1   MYELGHFIDGKRVAGTSGRVSNIFNPATGEVQGTVALASDADLAAAVESAKAAQPKWAAT 60
           M E+GHFI GKRVAGTSGR SN++NPATGEVQ TVALAS  +L AAV +AKAAQPKW AT
Sbjct: 1   MREIGHFIGGKRVAGTSGRTSNVYNPATGEVQATVALASVDELRAAVANAKAAQPKWGAT 60

Query: 61  NPQRRARVFMKFVQLLNDNMNELAEMLSREHGKTIDDAKGDIVRGLEVCEFVIGIPHLQK 120
           NPQRRARVF +FV+LLN NM+ELA +LS EHGKT++D+KGDI+RGLEVCEFV GIPHLQK
Sbjct: 61  NPQRRARVFFRFVELLNQNMDELATLLSSEHGKTVEDSKGDIIRGLEVCEFVCGIPHLQK 120

Query: 121 SEFTEGAGPGIDMYSIRQPVGIGAGITPFNFPGMIPMWMFAPAIACGNAFILKPSERDPS 180
            EFTEGAGP IDMYSIRQPVG+GAGITPFNFPGMIPMWMFAPAIACGNAFILKPSERDPS
Sbjct: 121 GEFTEGAGPAIDMYSIRQPVGVGAGITPFNFPGMIPMWMFAPAIACGNAFILKPSERDPS 180

Query: 181 VPIRLAELMIEAGLPAGILNVVNGDKGAVDAILTHPDIAAVSFVGSTPIARYVYGTAAMN 240
           +PIRLAELMIEAGLPAGILNVVNGDK AVDAILT PDIAAVSFVGSTPIARYVYGTAAMN
Sbjct: 181 LPIRLAELMIEAGLPAGILNVVNGDKTAVDAILTDPDIAAVSFVGSTPIARYVYGTAAMN 240

Query: 241 GKRAQCFGGAKNHMIIMPDADLDQAANALIGAGYGSAGERCMAISVAVPVGEETANRLID 300
           GKRAQCFGGAKNHMIIMPDAD+DQA NAL+GAGYGSAGERCMA+SVAVPVGE+TANRL++
Sbjct: 241 GKRAQCFGGAKNHMIIMPDADMDQAVNALMGAGYGSAGERCMAVSVAVPVGEDTANRLVE 300

Query: 301 KLVPMVESLRIGPYTDEKADMGPVVTKEAEQRIRSLIDSGIEQGAKLVVDGRDFKLQGYE 360
           KLVP +ESLRIGPYTD+KADMGP+VTKEA  R+  LID G+E+GAKLVVDGR FKLQGYE
Sbjct: 301 KLVPKIESLRIGPYTDDKADMGPLVTKEAYNRVNGLIDRGVEEGAKLVVDGRGFKLQGYE 360

Query: 361 NGHFIGGCLFDDVTPDMDIYKTEIFGPVLSVVRARNYEEALSLPMKHEYGNGVAIYTRDG 420
            G+F+GG LFD V PDMDIYKTEIFGPVLSVVRA+NYEEAL LPMKHEYGNGVAIYTRDG
Sbjct: 361 EGYFVGGTLFDHVKPDMDIYKTEIFGPVLSVVRAKNYEEALELPMKHEYGNGVAIYTRDG 420

Query: 421 DAARDFASRINIGMVGVNVPIPVPLAYHSFGGWKSSSFGDLNQHGTDSIKFWTRTKTITS 480
           DAARDFASRINIGM+GVNVPIPVPLAYHSFGGWK+SSFGDLNQHGTDSIKFWTRTKTIT+
Sbjct: 421 DAARDFASRINIGMIGVNVPIPVPLAYHSFGGWKASSFGDLNQHGTDSIKFWTRTKTITA 480

Query: 481 RWPSGIKDGAEFSIPTMR 498
           RWPSGIKDGAEF +PTM+
Sbjct: 481 RWPSGIKDGAEFVMPTMK 498


Lambda     K      H
   0.319    0.137    0.409 

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: 921
Number of extensions: 21
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: 498
Length of database: 498
Length adjustment: 34
Effective length of query: 464
Effective length of database: 464
Effective search space:   215296
Effective search space used:   215296
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 (21.7 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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