GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serB in Shewanella amazonensis SB2B

Align 2-oxoglutarate reductase; EC 1.1.1.399; EC 1.1.1.95; EC 3.1.3.3 (characterized, see rationale)
to candidate 6938846 Sama_2949 D-3-phosphoglycerate dehydrogenase (RefSeq)

Query= uniprot:L0G228_ECHVK
         (630 letters)



>FitnessBrowser__SB2B:6938846
          Length = 409

 Score =  420 bits (1079), Expect = e-122
 Identities = 205/407 (50%), Positives = 286/407 (70%), Gaps = 1/407 (0%)

Query: 225 KFSYPKSRINVLLLENVHPIGVEIMKQEGY-NVEVVSSAMSEEELCEKIKNVSIIGIRSK 283
           K S  K +I  LLLE VH   V+++++ GY N+E   +++++E L   IK+   +GIRS+
Sbjct: 3   KHSLDKDKIKFLLLEGVHQSAVDVLERAGYTNIEYHKASLADEALVASIKDAHFVGIRSR 62

Query: 284 TQITKKVLENANRLMAVGAFCIGTNQIDLETCQEKGIAVFNAPFSNTRSVVELAISEIIF 343
           TQ++ +VL  A +L+ +G FCIGTNQ+DL++ +  GI VFNAPFSNTRSV EL + EII 
Sbjct: 63  TQLSAEVLSKAEKLVGIGCFCIGTNQVDLKSAELAGIPVFNAPFSNTRSVAELVLGEIIM 122

Query: 344 LMRNLHDKTLKMHQGIWNKSASGSFEVRGKKLGIIGYGNIGAQLSVLAENMGMNVFYYDI 403
           LMR +  +    H+G W KSA+GS EVRGK LG+IGYG+IG QL +LAE +GM V ++DI
Sbjct: 123 LMRGIPQRNALCHRGGWLKSANGSVEVRGKTLGVIGYGHIGTQLGILAETLGMRVKFFDI 182

Query: 404 VERLALGNATKIDSLDELLETCDIISLHVDGRTENKNILNKEKIFKMKKGAILVNLSRGH 463
            ++L LGNA ++ S +ELL   D++SLHV    + KN++   ++  MKKG+ L+N SRG 
Sbjct: 183 EDKLPLGNAQQVHSFEELLANADVVSLHVPETPQTKNMIGHTELATMKKGSFLINASRGT 242

Query: 464 VVDVPALRDALESGHLAGAAVDVFPTEPKNNDEPFESELIGCPNTILTPHIGGSTLEAQE 523
           VVD+ AL  AL+  H+AGAA+DVFP EPK+ND+ F+S L G  N ILTPH+GGST EAQE
Sbjct: 243 VVDIDALSAALKEEHIAGAAIDVFPVEPKSNDDVFQSPLRGLDNVILTPHVGGSTEEAQE 302

Query: 524 NIAQFVPGKIIEYINSGNTFNSVNFPNIQLPFLKDAHRLIHIHQNAPGVLAKINQVLASY 583
           NI   V GK+ +Y ++G+T ++VNFP + LP  K   RL+HIH+N PG+L KINQ  +  
Sbjct: 303 NIGIEVAGKLAKYSDNGSTVSAVNFPEVSLPMHKGTSRLLHIHKNRPGILIKINQAFSEK 362

Query: 584 KINIVGQYLKTNEKIGYVITDIDKRYSNDVIDALKEIEGTIRFRILY 630
            INI  QYL+T   IGYV+ ++D   + + ++ L+ IEGTIR R+L+
Sbjct: 363 GINISAQYLQTTADIGYVVMEVDTHQAEEALEQLRGIEGTIRTRLLH 409


Lambda     K      H
   0.317    0.136    0.377 

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: 648
Number of extensions: 20
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: 630
Length of database: 409
Length adjustment: 34
Effective length of query: 596
Effective length of database: 375
Effective search space:   223500
Effective search space used:   223500
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 (21.6 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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