GapMind for catabolism of small carbon sources

 

Alignments for a candidate for puuC in Sinorhizobium meliloti 1021

Align gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate SMa1415 SMa1415 aldehyde dehydrogenase

Query= reanno::pseudo6_N2E2:Pf6N2E2_4383
         (497 letters)



>FitnessBrowser__Smeli:SMa1415
          Length = 498

 Score =  372 bits (956), Expect = e-107
 Identities = 209/483 (43%), Positives = 296/483 (61%), Gaps = 20/483 (4%)

Query: 23  FINGEYTDAVSGETFDCL-SPVDGRLLGKIASCDVADAQRAVENARATFSSGVWSRLAPS 81
           F++G++    SG  F    SP  G  + + A C V D   AV  AR  F    WS L   
Sbjct: 20  FVDGKWQ---SGHDFFVRHSPGHGVAVTRTAKCSVDDLNAAVAAARRAFEDRRWSGLPGG 76

Query: 82  KRKATMIRFAGLLKQHAEELALLETLDMGKPISDSLN-ID------VPGAAQALSWSGEA 134
            R + ++R A +L+   +ELA  ETL+ GKPI+ +   ID        GA  A    G++
Sbjct: 77  SRASVLLRVAEILRTRRDELAYWETLENGKPIAQARGEIDHCIACFEVGAGAARLLHGDS 136

Query: 135 IDKLYDEVAATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGPALSTGNSVVLKPSE 194
            + L D +        G+V REP+GVVG I PWNFP ++ C ++   L++G ++V+KPSE
Sbjct: 137 FNSLGDGL-------FGMVLREPIGVVGLITPWNFPFLILCERVPFILASGCTMVVKPSE 189

Query: 195 KSPLTALRIAALAIEAGIPKGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMI 254
            +  T L +A +  EAG+P GV NV+ G G T+G+A++ H D+D L FTGST + +  + 
Sbjct: 190 VTSATTLILAEVLAEAGLPDGVYNVITGSGRTIGQAMSEHPDIDMLSFTGSTAVGRSCVH 249

Query: 255 YSGESNMKRIWLEAGGKSPNIVFADAPDLQAAAESAASAIAFNQGEVCTAGSRLLVERSI 314
            + +SN K++ LE GGK+P IVFAD+ DL+ AA+ AA  I+FN G+ C + SRL+VERS+
Sbjct: 250 AAADSNFKKLGLELGGKNPIIVFADS-DLEDAADGAAFGISFNTGQCCVSSSRLIVERSV 308

Query: 315 KDTFLPLVIEALKGWKPGNPLDPATNVGALVDTQQMNTVLSYIEAGHSDGAKLVAGGKRI 374
              F  L+ E +K  + G+PLD  T VGA+    Q  T+L YI  G ++GA+LV GG  I
Sbjct: 309 AREFEALLAEKMKRIRVGDPLDETTQVGAITTEAQNTTILDYIAKGKTEGAELVTGGTAI 368

Query: 375 LEETGGTYVEPTIFDGVSNAMKIAQEEIFGPVLSVIAFDTAEQAIEIANDTPYGLAAAVW 434
            +   G Y+ PT+F GVS  M IA++EIFGPVL  + FDT EQA+E+ANDT YGLAA+VW
Sbjct: 369 -DLGRGQYIAPTLFSGVSREMAIARDEIFGPVLCSMTFDTVEQAVELANDTVYGLAASVW 427

Query: 435 TKDISKAHLTAKALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHAFDKYTELKSTW 494
           TK+I KA    + +RAG  WVN    G    P GGFKQSG GR+  ++  ++YT++KS  
Sbjct: 428 TKNIDKALTVTRRVRAGRFWVNTMMAGGPEMPLGGFKQSGWGREAGMYGVEEYTQVKSVH 487

Query: 495 IKL 497
           +++
Sbjct: 488 VEI 490


Lambda     K      H
   0.316    0.132    0.389 

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: 584
Number of extensions: 20
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: 497
Length of database: 498
Length adjustment: 34
Effective length of query: 463
Effective length of database: 464
Effective search space:   214832
Effective search space used:   214832
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.

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