GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Sinorhizobium meliloti 1021

Align Gamma-aminobutyrate:alpha-ketoglutarate aminotransferase (EC 2.6.1.19) (characterized)
to candidate SMa1855 SMa1855 hypothetical protein

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



>FitnessBrowser__Smeli:SMa1855
          Length = 458

 Score =  338 bits (867), Expect = 2e-97
 Identities = 183/447 (40%), Positives = 261/447 (58%), Gaps = 5/447 (1%)

Query: 10  SALQAMDAAHHLHPFTDSADLAKRGTRVIERAEGVYIWDAKGNKLLDAMAGLWCVNVGYG 69
           ++L  +D AH +HP        K G RV+  A+G  + DA G +L+D  AGLWCVN GYG
Sbjct: 4   NSLIELDRAHLIHPVASYRGHEKLGVRVLASAKGATVTDASGRQLIDGFAGLWCVNAGYG 63

Query: 70  RKSIADAAYAQLQTLPFYNNFFQCTHEPAIRLASKIASLAPGHMNRVFFTGSGSEANDTN 129
           +++I +AA  Q++ L +   +F    EPAIRLAS++A  APG++N V+FT  GS+A D+ 
Sbjct: 64  QETIVEAAAKQMRELSYATAYFGLGSEPAIRLASELAERAPGNLNHVYFTLGGSDAVDST 123

Query: 130 LRMVRRYWDLKGMPSKKTIISRKNAYHGSTVAGASLGGMGFMHQQGDLPIPGIVHIDQPY 189
           +R +R YW  +G P +   IS +  YHGS+  GA L  +   H    +P      I   Y
Sbjct: 124 IRFIRYYWTARGEPQRDQFISVEQGYHGSSTVGAGLTALPAFHTGFGIPFDWQHKIPSHY 183

Query: 190 WFGEGRDMSPEAFGIKTAQALEAKILELGEDKVAAFIAEPFQGAGGVIIPPDSYWNEIKR 249
            +       P+A    +  AL  K+ E+G ++VAAF AEP QG+GGV++PP  +   ++ 
Sbjct: 184 AYRNPVGDDPQAIIAASLTALRRKVEEIGPERVAAFYAEPIQGSGGVLVPPRGWMKAMRE 243

Query: 250 ILEKYNILFILDEVISGFGRTGNWFAAQTLGLKPDLITIAKGMTSGYIPMGGVIVSDRVA 309
           +     ILF+ DEVI+GFGRTG  FA+    + PD IT AKG+TSGY+PMG V ++D + 
Sbjct: 244 LCRDLGILFVADEVITGFGRTGPLFASTENEIVPDFITTAKGLTSGYVPMGAVFMADHIY 303

Query: 310 DVLISDGGEFA--HGFTYSGHPVAAAVALENIRILEEERLVDKVRTDTGPYLQDRLQTLS 367
             +    G  A  HG+TYS HPV+AAV LE +R+ E   L + V+   G  L + L +L 
Sbjct: 304 QTIADGAGASAVGHGYTYSAHPVSAAVGLEVLRLYENGLLENGVK--AGARLMEGLGSLR 361

Query: 368 AHPLVGEVRGMGMVGAIELVADKHSMVRFGSEISAGMLCREACIESGLVMRAVGDTMI-I 426
            HPLVG+VRG GM+ AIELV DK       +         +   E+GLV+RA  + ++  
Sbjct: 362 DHPLVGDVRGRGMLAAIELVVDKAQKTPLPAAAEPARRIFDRAWENGLVIRAFANGVLGY 421

Query: 427 SPPLCITRDEIDELIFKASQALSLTLE 453
           +PPLC +  EID +I +  Q+L  TLE
Sbjct: 422 APPLCCSETEIDAIIERTRQSLDETLE 448


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: 562
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: 458
Length adjustment: 33
Effective length of query: 427
Effective length of database: 425
Effective search space:   181475
Effective search space used:   181475
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.

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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