GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdG in Pseudomonas litoralis 2SM5

Align succinyl-CoA-glutarate CoA-transferase (EC 2.8.3.13) (characterized)
to candidate WP_090274851.1 BLU11_RS15305 CoA transferase

Query= reanno::pseudo5_N2C3_1:AO356_10845
         (406 letters)



>NCBI__GCF_900105005.1:WP_090274851.1
          Length = 746

 Score =  111 bits (277), Expect = 8e-29
 Identities = 108/406 (26%), Positives = 166/406 (40%), Gaps = 48/406 (11%)

Query: 4   LSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTEA 63
           L  L+VLDL   LAGP+A  +LADLGA+VIKVE P  GD  R     F    RG      
Sbjct: 384 LHGLKVLDLGAYLAGPFACMMLADLGAEVIKVEAPA-GDAMRRLERIFSGTQRG------ 436

Query: 64  AYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAINP 123
                    K  V +       Q  V  L   +D++  N ++       +DYD LK INP
Sbjct: 437 ---------KLGVALKLGDELSQPAVEALVRWADVVHHNMRLPAARKLQVDYDCLKLINP 487

Query: 124 QLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDILTG 183
           QL+YC ++ +G TGP A   G+D ++Q   G        +G  G  P+ +   + D   G
Sbjct: 488 QLLYCHVSAYGPTGPRADWPGFDQLMQASCGWEV----EQGGAGQPPMWLRFGVGDFFAG 543

Query: 184 LYSTAAILAALAHRDHVGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPNIV 243
           L S   +L  L  R   G GQ ++ +LL   +  ++        +      L      + 
Sbjct: 544 LSSLYVLLLGLYQRARTGEGQMVNASLLGATLLTMSEAVAREDGSVTPIAHLDATQTGLC 603

Query: 244 -PYQDFPTADGDFILTVGNDGQFRKFAEVAGQPQWADDPRFATNKVRVANRAVLIPLIRQ 302
             ++ +  +DG   +      + ++F  +AG          A  +V  A           
Sbjct: 604 DTHRLYCCSDGWVAVAALAPEEAQRFHALAG----------ADPEVHFA----------- 642

Query: 303 ATVFKTTAEWVTQLEQAGVPCGPIND--LAQVFADPQVQARGLAMELPHLLAGKVPQVAS 360
               +T  E +  L    VP   + +  L     +P   A GL     H   G++ Q+ +
Sbjct: 643 ---AQTQTEALLSLSAHDVPAEAVLEAQLDPFLDNPDHAAAGLHTRYQHAEYGELQQIGA 699

Query: 361 PIRLSETPVEYRNAPPLLGEHTLEVLQRVLGLDEAAVMAFREAGVL 406
                + P+     PP LG+H+ EVL   LG+ +  +     AGV+
Sbjct: 700 FWDFGDLPLSLDRPPPALGQHSREVLGG-LGIGDIELDRLAAAGVV 744



 Score = 79.7 bits (195), Expect = 3e-19
 Identities = 93/387 (24%), Positives = 141/387 (36%), Gaps = 55/387 (14%)

Query: 4   LSHLRVLDLSRVLAGPWAGQILADLGADVIKVERPGNGDDTRAWGPPFLKDARGENTTEA 63
           L  LRV+ L   +A   AG  L + GA+VI VE PGN              AR +     
Sbjct: 6   LHGLRVVSLGSGIASAAAGLHLCEAGAEVILVEPPGN-------------PARRQE---- 48

Query: 64  AYYLSANRNKQSVTIDFTRPEGQRLVRELAAKSDILIENFKVGGLAAYGLDYDSLKAINP 123
           A +   NR K+SVT+D   P+GQ+ + +L A +D+ I  F     A   L    L    P
Sbjct: 49  ALFAVLNRGKRSVTLDIDVPDGQQQLEQLLAAADVFIHEFTSKQAATLTLGDAQLAERFP 108

Query: 124 QLIYCSITGFGQTGPYAKRAGYDFMIQGLGGLMSLTGRPEGDEGAGPVKVGVALTDILTG 183
            LI  +ITG+ +  P A+    + ++    GL+      +     GPV V +   + L  
Sbjct: 109 GLIVSAITGWPKKHPLAEAMPRETLVLARLGLLD----EQPGHREGPVFVRMPFANWLAS 164

Query: 184 LYSTAAILAALAHRDH--VGGGQHIDMALLDVQVACLANQAMNYLTTGNAPKRLGNAHPN 241
                 ++A L  RD    GG  H  +A      A L    M++                
Sbjct: 165 WLCVVGVMARLIARDRDGQGGSAHTSLA-----QAALVPMTMHWSRAEKPTPAFAKGLDK 219

Query: 242 IVPYQDFPTADGDFILTVGNDGQFRKFAEVAGQ----------PQWADD---PRFATNKV 288
            +P      ADG +I    +  +    A+   +           QW      P F  N+ 
Sbjct: 220 HIPIPLHQCADGRWIHVHYSPDKSPWMADAMAELGEAEVARLNAQWPPSHVAPNFGANRA 279

Query: 289 RVANRAVLIPLIRQATVFKTTAEWVTQLEQAGVPCGPINDLAQVFADPQVQARGLAMELP 348
            +A R              +  EWV    Q  V          ++ D Q +  G  +E+ 
Sbjct: 280 IIATR--------------SAQEWVEHFWQHDVSAQIAAPFGDIYFDEQARLNGYVVEVE 325

Query: 349 HLLAGKVPQVASPIRLSETPVEYRNAP 375
               GK  Q     +++      R+AP
Sbjct: 326 DATLGKTLQPGPAWKITPPARIGRSAP 352


Lambda     K      H
   0.319    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: 727
Number of extensions: 42
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 406
Length of database: 746
Length adjustment: 36
Effective length of query: 370
Effective length of database: 710
Effective search space:   262700
Effective search space used:   262700
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 (21.7 bits)
S2: 53 (25.0 bits)

This GapMind analysis is from Sep 24 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