GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gabT in Azospirillum brasilense Sp245

Align Gamma aminobutyrate transaminase 3, chloroplastic; Gamma-aminobutyrate transaminase isozyme 3; LeGABA-TP3; SlGABA-T3; EC 2.6.1.96 (characterized)
to candidate AZOBR_RS03635 AZOBR_RS03635 aminotransferase

Query= SwissProt::Q84P52
         (520 letters)



>FitnessBrowser__azobra:AZOBR_RS03635
          Length = 471

 Score =  469 bits (1207), Expect = e-136
 Identities = 229/433 (52%), Positives = 308/433 (71%), Gaps = 3/433 (0%)

Query: 70  LAPFTAGWHSTDLE-PLVIQKSEGSYVYDVNGKKYLDALAGLWCTSLGGNEPRLVAAATK 128
           L P+T   H+ + + PL+I++ EG  V+D +GK+Y++ LA LWC SLG  E RLV AAT+
Sbjct: 32  LHPYT-NLHAHETQGPLIIERGEGVRVFDDSGKEYIEGLASLWCVSLGWGEERLVEAATR 90

Query: 129 QLNELAFYHSFWNRSTKPSLDLAKELLDLFTANKMAKAFFTNSGSEANDTQVKLVWYYNN 188
           Q+ +L  YH F ++S +P +DLA+ L+ L     M+K FF NSGSEANDT VKLVWYYNN
Sbjct: 91  QMRKLPTYHVFGHKSHEPGIDLAERLIKLAPV-PMSKVFFANSGSEANDTAVKLVWYYNN 149

Query: 189 ALGRPDKKKFIARTKSYHGSTLISASLSGLPALHQQFDLPAPFVLHTDCPHFWRFHQPGE 248
           ALGRP+KKK ++R K+YHG T+ +ASL+GL   H+ FDLP   + HTDCPH +RF +PGE
Sbjct: 150 ALGRPEKKKILSRVKAYHGVTVATASLTGLVNNHRDFDLPIARIQHTDCPHHYRFAEPGE 209

Query: 249 TEEEFSTRLANNLENLILKEGPETIAAFIAEPVMGAGGVIPPPATYFEKVQAILKKYDIL 308
           +EE+F+TRLA +LE LIL EGPETIAA  AEPVMGAGGVI PPATYF K+Q ILKKYDIL
Sbjct: 210 SEEDFATRLAESLEALILAEGPETIAAMFAEPVMGAGGVIVPPATYFAKIQPILKKYDIL 269

Query: 309 FIADEVICGFGRLGTMFGCEKYNIKPDLVSVAKALSSGYMPIGAVLVSPEVSDVIYSQSN 368
            +ADEVICGFGR G  +G +   ++PD+++ AK LSSGY+PI AV+VS  V      +S 
Sbjct: 270 LVADEVICGFGRTGNFWGSQTMGMQPDILTCAKQLSSGYLPISAVMVSDAVYRACVEESK 329

Query: 369 KLGTFSHGFTYSGHPVSCAVALETLKIYKERNIIEQVNRISPKFQEGLKAFSDSPIIGEI 428
           K+GTF HG+TYS HPV+ AVA+ETLKIY+ER+++  V  ++P FQ  LKA +D P++GE 
Sbjct: 330 KIGTFGHGYTYSAHPVAAAVAIETLKIYEERDLVGHVRAVAPLFQRRLKALADHPLVGEA 389

Query: 429 RGTGLLHGTEFTDNKSPNDPFPPEWGIGAYFGARCEKHGVLVRVAGDNIMMSPPYILSLE 488
           RG GL+   E   +K    PF P    GA      +++G+++R  GD++ + PP ++  E
Sbjct: 390 RGVGLIGALELVADKETKTPFDPVGRAGAVVNGLSQENGLIIRAMGDSVAVCPPLVIGEE 449

Query: 489 EIDELIIKYGKAL 501
           +I+ +  +   AL
Sbjct: 450 DINRMFDRLTTAL 462


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: 645
Number of extensions: 18
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: 471
Length adjustment: 34
Effective length of query: 486
Effective length of database: 437
Effective search space:   212382
Effective search space used:   212382
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