GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Sinorhizobium meliloti 1021

Align Gamma aminobutyrate transaminase 3, chloroplastic; Gamma-aminobutyrate transaminase isozyme 3; LeGABA-TP3; SlGABA-T3; EC 2.6.1.96 (characterized)
to candidate SM_b20379 SM_b20379 aminotransferase

Query= SwissProt::Q84P52
         (520 letters)



>FitnessBrowser__Smeli:SM_b20379
          Length = 461

 Score =  497 bits (1280), Expect = e-145
 Identities = 239/436 (54%), Positives = 315/436 (72%), Gaps = 1/436 (0%)

Query: 69  MLAPFTAGWHSTDLEPLVIQKSEGSYVYDVNGKKYLDALAGLWCTSLGGNEPRLVAAATK 128
           ++ P+T      +  P VI   +G YV D  GK+Y++ LAGL+C  LG +E RLV AAT+
Sbjct: 16  LVHPYTNLAVHQETGPHVITGGDGIYVVDDEGKRYIEGLAGLFCAGLGFSEQRLVEAATR 75

Query: 129 QLNELAFYHSFWNRSTKPSLDLAKELLDLFTANKMAKAFFTNSGSEANDTQVKLVWYYNN 188
           QL  + FYHSF ++ST+P + LA++LL +     M+K FF  SGSEANDT +KL+WYYNN
Sbjct: 76  QLKTMPFYHSFAHKSTEPGIRLAEKLLSIAPV-PMSKVFFAGSGSEANDTAIKLIWYYNN 134

Query: 189 ALGRPDKKKFIARTKSYHGSTLISASLSGLPALHQQFDLPAPFVLHTDCPHFWRFHQPGE 248
           ALGRP+KKK I+R K+YHG T+ +ASL+GLP  H+ FDLP   +LHTDCPH+WRF + GE
Sbjct: 135 ALGRPEKKKIISRRKAYHGVTVATASLTGLPFNHRDFDLPIANILHTDCPHYWRFAETGE 194

Query: 249 TEEEFSTRLANNLENLILKEGPETIAAFIAEPVMGAGGVIPPPATYFEKVQAILKKYDIL 308
           TEE+F+TR+ANNLE +IL+EGPETIAAF AEPVM +GGVI PP TYFEKVQA+L+KYDIL
Sbjct: 195 TEEDFATRMANNLEAIILEEGPETIAAFFAEPVMVSGGVITPPKTYFEKVQAVLRKYDIL 254

Query: 309 FIADEVICGFGRLGTMFGCEKYNIKPDLVSVAKALSSGYMPIGAVLVSPEVSDVIYSQSN 368
            IADEVICGFGR G MFG E Y +KPD++S AK LS+ YMPI A++++ +++D +  QS 
Sbjct: 255 LIADEVICGFGRTGNMFGSETYGLKPDMISCAKQLSAAYMPISALMINAKIADALVDQSR 314

Query: 369 KLGTFSHGFTYSGHPVSCAVALETLKIYKERNIIEQVNRISPKFQEGLKAFSDSPIIGEI 428
           K+GTFSHGFTY GHPV+ AVALE L IY+E +I+  V  ++P FQ+ ++   + P+IGE 
Sbjct: 315 KIGTFSHGFTYGGHPVAAAVALEALTIYEEIDIVGHVRSVAPAFQDRVRKLGEHPLIGEA 374

Query: 429 RGTGLLHGTEFTDNKSPNDPFPPEWGIGAYFGARCEKHGVLVRVAGDNIMMSPPYILSLE 488
           RG GL+ G EF  +K+  + FPP W +    G      GVL R  GD + + P  I+  E
Sbjct: 375 RGVGLVAGLEFVKDKATRENFPPAWQVANQAGKFATARGVLTRGLGDMVSLCPAMIIDDE 434

Query: 489 EIDELIIKYGKALKDT 504
           +ID+L+ + G AL DT
Sbjct: 435 QIDDLMTRMGLALDDT 450


Lambda     K      H
   0.317    0.135    0.401 

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: 608
Number of extensions: 20
Number of successful extensions: 2
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: 520
Length of database: 461
Length adjustment: 34
Effective length of query: 486
Effective length of database: 427
Effective search space:   207522
Effective search space used:   207522
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.

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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