GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Azospirillum brasilense Sp245

Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate AZOBR_RS22505 AZOBR_RS22505 omega amino acid--pyruvate aminotransferase

Query= reanno::SB2B:6938540
         (460 letters)



>FitnessBrowser__azobra:AZOBR_RS22505
          Length = 436

 Score =  286 bits (731), Expect = 1e-81
 Identities = 163/440 (37%), Positives = 239/440 (54%), Gaps = 21/440 (4%)

Query: 20  HLHPFTDSADLAKRGTRVIERAEGVYIWDAKGNKLLDAMAGLWCVNVGYGRKSIADAAYA 79
           H  PFT + +  K   R+I RAEG + WDA+G K+ D+++GLWC   G+ R+ I++A   
Sbjct: 9   HWMPFTANREF-KANPRLIARAEGAWYWDAEGRKIYDSLSGLWCCGAGHSRREISEAVAR 67

Query: 80  QLQTLPFYNNFFQCTHEPAIRLASKIASLAPGHMNRVFFTGSGSEANDTNLRMVRRYWDL 139
           Q+  L  Y+  FQ  H  A +LA K+AS+ P  ++ VFF  SGSEA DT+L+M R YW L
Sbjct: 68  QIAELD-YSPAFQFGHPAAFKLAHKLASMTPAGLDHVFFVNSGSEATDTSLKMARAYWRL 126

Query: 140 KGMPSKKTIISRKNAYHGSTVAGASLGGMGFMHQQ--GDLPIPGIVHIDQPY-WFGEGRD 196
           KG P+K  +I R   YHG    G SLGG+G   +     +    + H   P   F +G  
Sbjct: 127 KGQPAKTKLIGRSKGYHGVNFGGISLGGIGGNRKLFGSGVEADHLPHTLLPQNAFTKGL- 185

Query: 197 MSPEAFGIKTAQALEAKILELGEDKVAAFIAEPFQGAGGVIIPPDSYWNEIKRILEKYNI 256
             PE  G + A ALE  +       +AA I EP  G+ GV+ PP  Y   ++ + +K+NI
Sbjct: 186 --PEQ-GAELADALEELVALHDASNIAAVIVEPLAGSAGVLPPPKGYLQRLRALCDKHNI 242

Query: 257 LFILDEVISGFGRTGNWFAAQTLGLKPDLITIAKGMTSGYIPMGGVIVSDRVADVLISDG 316
           L I DEVI+GFGR G  F A   G+ PD++ +AKG+T+G +PMG V+ +  +    + +G
Sbjct: 243 LLIFDEVITGFGRMGAAFGADAFGVVPDIMNVAKGLTNGAVPMGAVVANHEIYQTFMDNG 302

Query: 317 G-----EFAHGFTYSGHPVAAAVALENIRILEEERLVDKVRTDTGPYLQDRLQTLSAHPL 371
           G     EF HG+TYS HPVA A  L  + + E ++L +K   D  P+ +  L  L     
Sbjct: 303 GADYMVEFPHGYTYSAHPVACAAGLAALELFERDKLAEKA-ADLAPHFETVLHGLKGLRH 361

Query: 372 VGEVRGMGMVGAIELVADKHSMVRFGSEISAGMLCREACIESGLVMRAVGDTMIISPPLC 431
           V ++R  G+ GA+++ A      R   EI+        C ++G  +R  GDT+   P   
Sbjct: 362 VTDIRNYGLAGAVQIAALPGEPARRPYEIAM------KCWKAGFYVRFGGDTLQFGPHFI 415

Query: 432 ITRDEIDELIFKASQALSLT 451
             R+++D L+   S A+  T
Sbjct: 416 SEREDLDRLMNAVSDAIQAT 435


Lambda     K      H
   0.321    0.137    0.408 

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: 532
Number of extensions: 24
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: 460
Length of database: 436
Length adjustment: 33
Effective length of query: 427
Effective length of database: 403
Effective search space:   172081
Effective search space used:   172081
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 17 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