GapMind for catabolism of small carbon sources

 

Alignments for a candidate for mmsA in Herbaspirillum seropedicae SmR1

Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate HSERO_RS23245 HSERO_RS23245 methylmalonate-semialdehyde dehydrogenase

Query= metacyc::MONOMER-15203
         (503 letters)



>FitnessBrowser__HerbieS:HSERO_RS23245
          Length = 497

 Score =  674 bits (1740), Expect = 0.0
 Identities = 327/501 (65%), Positives = 398/501 (79%), Gaps = 4/501 (0%)

Query: 3   IKRIEHYINGHKTNGVADSHQEVTNPATGQVTGQVALASQADVDSAVAAAQAAFPAWSDT 62
           +++I HYI G + +  +  + +V NPA G    QVAL +  +VD+AV A  AAFPAWS+T
Sbjct: 1   MEKIAHYIGGQRVDTRSGRYADVFNPAQGVPVAQVALGTSDEVDAAVKAGVAAFPAWSNT 60

Query: 63  PPIRRARVMFKFLELLNAHKDELAEAITREHGKVFTDAQGEVARGIDIVEFACGIPQLLK 122
           PP+ RARV+F+FL L+    D+ A  I REHGK F+DAQGEVARGI+IVEFA GIPQ+LK
Sbjct: 61  PPLTRARVLFRFLHLIQQRADDFARIIVREHGKTFSDAQGEVARGIEIVEFAAGIPQMLK 120

Query: 123 GDYTEQVSTGIDNWTTRQPLGVVAGITPFNFPVMVPMWMFPLAIAAGNSFVLKPSPLDPS 182
           G+YT+Q++ GID W+ RQ LGVVAGITPFNFP MVPMWMFP+AIA GN FVLKPS  DPS
Sbjct: 121 GEYTDQIARGIDAWSMRQALGVVAGITPFNFPAMVPMWMFPIAIACGNCFVLKPSERDPS 180

Query: 183 ASLMMADLLKQAGLPDGVFNVVQGDKDSVEALIDHPDVKALSFVGSTPIANLIYERGARS 242
           ASL++ADLLK+AGLPDGVFNVVQGDK +V+AL+DHP VKA+SFVGSTPIA  IY RG+  
Sbjct: 181 ASLLIADLLKEAGLPDGVFNVVQGDKVTVDALLDHPQVKAISFVGSTPIAEYIYARGSAK 240

Query: 243 GKRIQALGGAKNHMVVMPDANLDKAVDALIGAAYGSAGERCMAISVAVLVGDVADKIVPR 302
           GKR+QALGGAKNHMVVMPDA++  AVDAL+GAAYGSAGERCMAISVA+ VG   D++V  
Sbjct: 241 GKRVQALGGAKNHMVVMPDADMQLAVDALMGAAYGSAGERCMAISVALAVGSAGDELVAA 300

Query: 303 LAERARDLKIKNGLELDAEMGPIVTSQAHQRITGYIEKGVAEGAEMVVDGRDFDSSVTGE 362
           LAERAR LKI  G+   AEMGP+VT+ A +RI G I +GV EGA +VVDGR +       
Sbjct: 301 LAERARKLKINEGMAAGAEMGPVVTAAAKERIEGLIGRGVEEGATLVVDGRGYQV----P 356

Query: 363 GCADGFWMGGTLFDHVTPEMTIYREEIFGPVLACVRVPDVATAIQLINDHEFGNGVSCFT 422
           G   GF++GGTL DHVTPEMT+Y+EEIFGPVL  +R PD+A+A++LIN HE+GNGV+ +T
Sbjct: 357 GFEKGFFVGGTLLDHVTPEMTVYKEEIFGPVLCVLRCPDIASAVELINAHEYGNGVAVYT 416

Query: 423 ESGSVAREFGRRIQVGMVGINVPIPVPMAWHGFGGWKRSMFGDTHAYGEEGVRFYTKQKS 482
             G VAREF R+I+VGMVG+NVP+PVPMA+  FGGWKRS+FGD H YG EGVRFYT+ K+
Sbjct: 417 RDGGVAREFVRQIEVGMVGVNVPLPVPMAFSSFGGWKRSLFGDHHMYGPEGVRFYTRAKA 476

Query: 483 IMQRWSDSIDAGAEFAMPTAK 503
           +MQRW ++  AGAEFA P  K
Sbjct: 477 VMQRWPNTASAGAEFAFPQMK 497


Lambda     K      H
   0.319    0.136    0.406 

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: 811
Number of extensions: 21
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: 503
Length of database: 497
Length adjustment: 34
Effective length of query: 469
Effective length of database: 463
Effective search space:   217147
Effective search space used:   217147
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 (21.8 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