GapMind for catabolism of small carbon sources

 

Alignments for a candidate for astC in Sphingobium czechense LL01

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate WP_066609126.1 V473_RS20290 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme

Query= reanno::Koxy:BWI76_RS11670
         (406 letters)



>NCBI__GCF_001046645.1:WP_066609126.1
          Length = 462

 Score =  144 bits (362), Expect = 7e-39
 Identities = 123/418 (29%), Positives = 195/418 (46%), Gaps = 57/418 (13%)

Query: 19  APAAFIPVRGEGSRLWDQQGKEYIDFAGGIAVNALGHAHPRLVKALTEQ------AGKFW 72
           A  A +   G+G  L D +G+E ID   G+    +G+    + +A  EQ      A  ++
Sbjct: 29  AHGALLLESGKGMWLKDVEGRELIDAFAGLWCVNVGYGQDSIAEAAAEQMRRLPYATGYF 88

Query: 73  HTGNGYTNEPVLRLAKQLIDAT--FADRVFFCNSGAEANEAALKLARKYAHDRFGS-EKS 129
           H G+    EP ++LA+QL+D +    D V+F   G++A ++A++    Y H+  G  EK 
Sbjct: 89  HFGS----EPAVKLAQQLVDLSPEGLDHVYFTLGGSDAVDSAIRYITHY-HNAIGKPEKK 143

Query: 130 GIVAFKNAFHGRTLFTVSAGGQPAYSQDFAPLPPQIQHAIYN------DLDSAKALI--- 180
             +A +  +HG +           + + F  LP + QH I +      DL+   A I   
Sbjct: 144 QFIALERGYHGSSSTGAGLTALANFHRGF-DLPLRWQHHIASPYPYRSDLEGDDAAIIAR 202

Query: 181 -------------DDNTCAVIVEPMQGEGGVVPADADFLRGLRELCDAHNALLIFDEVQT 227
                         DN  A   EP+QG GGV+     +L+ +RE C   + L + DEV T
Sbjct: 203 SVQELKDKVAQLGADNVAAFFCEPIQGSGGVIVPPVGWLKAMRETCTQLDILFVTDEVIT 262

Query: 228 GVGRTGELYAYMHYGVTPDLLSTAKALGGGF-PIGALLASER--------CASVMTVGTH 278
           G GRTG ++A    GVTPDL++ AK L  G+ P+GALL S +         A  + +G H
Sbjct: 263 GFGRTGPMFACEAEGVTPDLMTLAKGLTAGYVPMGALLMSGKVYEGIANGAAPEVAIG-H 321

Query: 279 GTTYGGNPLACAVAGEVFATINTREVLNGVKQRHQWFCERLNAINARYGLFKEIRGLGLL 338
           G TY G+P++ AV  EV        +L   ++    F   L  + A + +  + RG GLL
Sbjct: 322 GATYSGHPVSAAVGLEVLRLYTDGGILANGQRVATRFDAGLAGL-ANHPMVGDTRGRGLL 380

Query: 339 IGCVLKDEYAGKAK---------AISNQAAEEGLMILIAGANVVRFAPALIISEDEVN 387
               L  +   KA+          +  +A + G++      N++  APAL  S+ E++
Sbjct: 381 GAIELVADKGSKARFDPGLKLADRLFAKAYDNGVIFRAFADNIIGLAPALCASDGEMD 438


Lambda     K      H
   0.321    0.137    0.412 

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: 496
Number of extensions: 33
Number of successful extensions: 6
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: 406
Length of database: 462
Length adjustment: 32
Effective length of query: 374
Effective length of database: 430
Effective search space:   160820
Effective search space used:   160820
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: 51 (24.3 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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