GapMind for catabolism of small carbon sources

 

Aligments for a candidate for rocA in Caulobacter crescentus NA1000

Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate CCNA_00865 CCNA_00865 alpha-ketoglutaric semialdehyde dehydrogenase xylA

Query= BRENDA::Q9K9B2
         (515 letters)



>lcl|FitnessBrowser__Caulo:CCNA_00865 CCNA_00865 alpha-ketoglutaric
           semialdehyde dehydrogenase xylA
          Length = 478

 Score =  255 bits (652), Expect = 2e-72
 Identities = 157/474 (33%), Positives = 243/474 (51%), Gaps = 13/474 (2%)

Query: 41  INGERVTTEDKIQSWNPARKDQLVGSVSKANQDLAEKAIQSADEAFQTWRNVNPEERANI 100
           I GERV  +   +S NP+  + +V  V    Q   + A+ +A +AF  W + +PE R+++
Sbjct: 9   IGGERVAADAPAESLNPSNTNDVVAKVPMGGQAEVDAAVDAARKAFPAWADASPEVRSDL 68

Query: 101 LVKAAAIIRRRKHEFSAWLVHEAGKPWKEADADTAEAIDFLEYYARQMIELNRGKEILSR 160
           L K  + I  R  +    L  E GK   E   +T  A    +Y+A + +  +      +R
Sbjct: 69  LDKVGSTIIARSADIGRLLAREEGKTLAEGIGETVRAGRIFKYFAGEALRRHGQNLESTR 128

Query: 161 PGEQNRYFYTPMGVTVTISPWNFALAIMVGTAVAPIVTGNTVVLKPASTTPVVAAKFVEV 220
           PG + + +   +GV   I+PWNF +AI    A   +  GNTVV+KPA  TP  A    ++
Sbjct: 129 PGVEIQTYRQAVGVYGLITPWNFPIAIPAWKAAPALAFGNTVVIKPAGPTPATANVLADI 188

Query: 221 LEDAGLPKGVINYVPGSGAEVGDYLVDHPKTSLITFTGSKDVGVRLYERAAVVRPGQNHL 280
           + + G P GV N + G G+ +GD L+ H     ++FTGS+ VG ++   AAV R      
Sbjct: 189 MAECGAPAGVFNMLFGRGS-MGDALIKHKDVDGVSFTGSQGVGAQV-AAAAVARQA---- 242

Query: 281 KRVIVEMGGKDTVVVDRDADLDLAAESILVSAFGFSGQKCSAGSRAVIHKDVYDEVLEKT 340
            RV +EMGGK+ ++V  DADL+ A    L  +F  +GQ+C+A SR ++   ++D+ +   
Sbjct: 243 -RVQLEMGGKNPLIVLDDADLERAVAIALDGSFFATGQRCTASSRLIVQDGIHDKFVALL 301

Query: 341 VALAKNLTVGDPTNRDNYMGPVIDEKAFEKIMSYIEIGKKE-GRLMTGGEGD--SSTGFF 397
                 L VGD  + +  +GP + E   E    YI+I   E GR++TGG+     + G++
Sbjct: 302 AEKVAALRVGDALDPNTQIGPAVSEDQMETSYRYIDIAASEGGRVVTGGDRIKLDNPGWY 361

Query: 398 IQPTIIADLDPEAVIMQEEIFGPVVAFSKANDFDHALEIANNTEYGLTGAVITRNRAHIE 457
           ++PT+IAD      I  EE+FGPV +  +   ++ ALEIAN  E+GL+  + T +  H  
Sbjct: 362 VRPTLIADTQAGMRINNEEVFGPVASTIRVKSYEEALEIANGVEFGLSAGIATTSLKHAR 421

Query: 458 QAKREFHVGNLYFNRNCTGAIVGYH-PFGGFKMSGTDSKAGGPDYLALHMQAKT 510
             +R    G    N    G  V YH PFGG K S   ++  G   +    Q KT
Sbjct: 422 HFQRYARAGMTMVNLATAG--VDYHVPFGGTKSSSYGAREQGFAAVEFFTQTKT 473


Lambda     K      H
   0.316    0.134    0.388 

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: 590
Number of extensions: 28
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: 515
Length of database: 478
Length adjustment: 34
Effective length of query: 481
Effective length of database: 444
Effective search space:   213564
Effective search space used:   213564
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 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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