GapMind for catabolism of small carbon sources

 

Aligments for a candidate for praB in Herbaspirillum seropedicae SmR1

Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate HSERO_RS19755 HSERO_RS19755 betaine-aldehyde dehydrogenase

Query= metacyc::MONOMER-15108
         (486 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS19755 HSERO_RS19755
           betaine-aldehyde dehydrogenase
          Length = 484

 Score =  361 bits (926), Expect = e-104
 Identities = 196/481 (40%), Positives = 283/481 (58%), Gaps = 12/481 (2%)

Query: 13  HFIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNG-PWKKMTAN 71
           HFI G+   + DG+  + +NP  EE   + A+G AA++  AV AAK  L G  W K++  
Sbjct: 7   HFIAGEATEASDGQRMNLVNPINEEIYASAAQGTAADVARAVAAAKAQLEGGAWSKLSGL 66

Query: 72  ERIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYI-----R 126
           +R  +L K+  L+    + L+ +++   G+       +D+P A  +    + +      R
Sbjct: 67  QRGQLLHKLAALVERDTDLLADMDARAIGRSPMEPRMMDVPNAISHLRAAAGWANQMEGR 126

Query: 127 TITNEATQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELT 186
           TI   A  M    L+Y +R P+GV+G I PWN PL++ +WK+A  LAAG TVV+KPAE T
Sbjct: 127 TIPT-AGYMGKPTLSYTVREPIGVVGAILPWNAPLMITSWKVAALLAAGCTVVIKPAEET 185

Query: 187 PMTATVLAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMAS 246
           P +A  LA + ++AG PDGV+N+V G+G NS G AL EHPDV  ISFTG    G+ I   
Sbjct: 186 PQSALHLARLAQEAGFPDGVINVVTGYG-NSVGRALCEHPDVAKISFTGSPEAGRAIQRI 244

Query: 247 AAKTLKRLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEA 306
           A +  KR++ ELGGK+P ++F D+  ++ +       F+NQG+VC  GSRI V+R   + 
Sbjct: 245 AGEQFKRVTLELGGKSPQIVFDDAPFEDALFGCTLGLFVNQGQVCAAGSRILVQRSLAQR 304

Query: 307 FLEKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGG-KRPEG 365
           F +        + VGDP     ++G +     +ERV  YI+  ++EG T+L GG  RP+ 
Sbjct: 305 FAKALAEAAAGITVGDPSQPGVRMGPVAKKAQFERVNRYIQQGLDEGATLLAGGVSRPD- 363

Query: 366 LEKGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTN 425
             KG+F++PTI         + +EEIFGPV T+I FDTEEE +   ND+ YGL+A+VWT 
Sbjct: 364 --KGWFVQPTIFADANNGMSIAREEIFGPVGTIISFDTEEEAIALANDSKYGLAATVWTT 421

Query: 426 DLRRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNICIK 485
           +L RAHRVA  ++ G V VN W   D   P+GG+K SG+GREGGL     Y+E   + + 
Sbjct: 422 NLARAHRVAAGVKVGAVGVNCWSPLDANLPWGGIKDSGMGREGGLAGALAYTEEKTVTVL 481

Query: 486 L 486
           L
Sbjct: 482 L 482


Lambda     K      H
   0.318    0.136    0.404 

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: 592
Number of extensions: 29
Number of successful extensions: 4
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: 486
Length of database: 484
Length adjustment: 34
Effective length of query: 452
Effective length of database: 450
Effective search space:   203400
Effective search space used:   203400
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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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