GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Herbaspirillum seropedicae SmR1

Align 4-aminobutyrate-2-oxoglutarate transaminase (EC 2.6.1.19); 4-aminobutyrate-pyruvate transaminase (EC 2.6.1.96) (characterized)
to candidate HSERO_RS17580 HSERO_RS17580 hypothetical protein

Query= BRENDA::Q94CE5
         (504 letters)



>FitnessBrowser__HerbieS:HSERO_RS17580
          Length = 440

 Score =  245 bits (625), Expect = 3e-69
 Identities = 148/433 (34%), Positives = 231/433 (53%), Gaps = 19/433 (4%)

Query: 70  PLVIAKSEGSYVYDDTGKKYLDSLAGLWCTALGGNEPRLVSAAVEQLNTLPFYH-SFWNR 128
           P+ +A  EG  + D  GK+Y+D+  G   + LG   PR++ A  +Q+  L + H SF+  
Sbjct: 14  PMAVA-GEGMELIDQDGKRYIDASGGAAVSCLGHGHPRVIEAIRKQVGELAYAHTSFF-- 70

Query: 129 TTKPSLDLAKVLLEMFTANKMAKAFFTSGGSDANDTQVKLVWYYNNALGRPEKKKFIARK 188
           TT P+ +LA +L +      +   +F SGGS+A +  +KL   Y   +G+P+++  IAR+
Sbjct: 71  TTAPAEELAAMLADA-APGSLNHVYFLSGGSEAVEAALKLARQYYVEVGQPQRRHIIARR 129

Query: 189 KSYHGSTLISASLSGLPPLHQNFDLPAPFVLHTDCPHY-WRFHLPGETEEEFSTRLAKNL 247
           +SYHG+TL + ++ G     + F +P     H   P Y +R    GE++ ++  RLA  L
Sbjct: 130 QSYHGNTLGALAIGGNAWRREMF-MPMLIEAHHVSPCYAYRNRADGESDVQYVQRLADEL 188

Query: 248 EDLIIKEGPETIGAFIAEPVMGA-GGVIPPPATYFEKVQAVVKKYDILFIADEVICAFGR 306
           E  I+  G + + AF+AE V+GA  G +PP   YF K++AV  KY +L I DEV+   GR
Sbjct: 189 EQKILSLGADQVIAFVAETVVGATAGAVPPVGDYFRKIRAVCDKYGVLLILDEVMSGMGR 248

Query: 307 LGTMFGCDKYNIKPDLVTLAKALSSAYMPIGAILMSQEVADVINSHSSKLGVFSHGFTYS 366
            G +F C++  + PD+V +AK L + Y PIGA++ S  + D +   S   G F HG TY 
Sbjct: 249 TGYLFACEEDGVVPDIVVIAKGLGAGYQPIGAMICSDHIYDAVLRGS---GFFQHGHTYI 305

Query: 367 GHPVSCAVAIEALKIYKERNIPEYVAKVAPRFQDGVKAFASGSPIIGETRGTGLILGTEF 426
           GH  +CA A+   K  +E  + E V +   + +  ++        +G+ RG GL +G E 
Sbjct: 306 GHATACAAAVAVQKTIQEERLLENVRQRGEQLRSELRQAFGDQAHVGDIRGRGLFVGVEL 365

Query: 427 VDNKSPNEPFPPEWGVGAFFGAECQKHGMLVRVA--------GDGILMSPPLIISPEEID 478
           V  +S   P  P+    A   AE  K G+LV           GD IL++PP I S  +I 
Sbjct: 366 VAERSSKLPLSPDLRTHARVKAEAMKRGLLVYPMGGTIDGKNGDHILLAPPFIASSNDIS 425

Query: 479 ELISIYGKALKAT 491
           E++     A+ A+
Sbjct: 426 EIVQRLSDAVAAS 438


Lambda     K      H
   0.318    0.135    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: 523
Number of extensions: 26
Number of successful extensions: 5
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: 504
Length of database: 440
Length adjustment: 33
Effective length of query: 471
Effective length of database: 407
Effective search space:   191697
Effective search space used:   191697
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: 51 (24.3 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