GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpE in Rhizobium etli CFN 42

Align Acyl-coenzyme A synthetase ACSM3, mitochondrial; Acyl-CoA synthetase medium-chain family member 3; Butyrate--CoA ligase 3; Butyryl-coenzyme A synthetase 3; Middle-chain acyl-CoA synthetase 3; Propionate--CoA ligase; Protein SA homolog; EC 6.2.1.2; EC 6.2.1.17 (characterized)
to candidate WP_011426974.1 RHE_RS19290 AMP-binding protein

Query= SwissProt::Q3UNX5
         (580 letters)



>NCBI__GCF_000092045.1:WP_011426974.1
          Length = 550

 Score =  251 bits (642), Expect = 4e-71
 Identities = 180/557 (32%), Positives = 275/557 (49%), Gaps = 38/557 (6%)

Query: 33  NFSNYESMKQDFKIEIPEYFNFAKDVLDQWTNMEKAGKRLSNPAFWWIDGNGEELRWSFE 92
           +F  Y  + +DF   IPE FN  + V D+W   +     L +        NG+ L  ++ 
Sbjct: 5   SFDRYGDLYRDFSWRIPEDFNIGRAVSDEWAARDPERVCLEH-----FSPNGDHLSLTYG 59

Query: 93  ELGLLSRKFANILTEACSLQRGDRVMVILPKIPEWWLANVACLRTGTVLIPGTTQLTQKD 152
           EL   S  FAN L  +  ++RGDRV +++P+  E  +A+VA  + G + +P       + 
Sbjct: 60  ELSAASSMFANALA-SLGIKRGDRVALLVPQSFETVIAHVAIYKIGAIALPLALLFGVEA 118

Query: 153 ILYRLQSSKAKCIITDDTLAPAVDAVAAKCENLHSKLIVSQHSREGWGNLKEMMKYAS-- 210
           + YRL+ S A  IIT+D     V  +  +   L   + VS  +        + + +A   
Sbjct: 119 LEYRLRISGAAAIITNDFGLDRVRQIRDRLPELRHVISVSDAA--------DALSFADLI 170

Query: 211 DSHTCV----DTKHDEMMAIYFTSGTTGPPKMIGHTHSSF-----GLGLSVNGRFWLDLI 261
            SH  V     T  D+   + FTSGTTGPPK   H H        G+  +  G   +   
Sbjct: 171 ASHASVFEGEKTTPDDAALMIFTSGTTGPPKGALHGHRVLPGHIPGMQFAHEGFPKV--- 227

Query: 262 ASDVMWNTSDTGWAKSAWSSVFSPWTQGACVFAHYLPRFESTSILQTLSKFPITVFCSAP 321
             D +W  SD  WA    +++      G  V +    +F++ +  + +++  +      P
Sbjct: 228 -GDKVWTPSDWAWAGGLLNALLPSLLLGVPVVSSPAQKFDADTAYRIMAEMKVRNAFIPP 286

Query: 322 TAYRML--VQNDMSSYKFNSLKHCVSAGEPINPEVMEQWRKKTGLDIYEGYGQTETVLIC 379
           TA R++  V +  S Y    L+   SAGE +  E  +  R+  G+ + E YGQTE   + 
Sbjct: 287 TALRLMRSVSDPRSKYDL-VLRTVGSAGEALGRETYDWARRTLGITVNEFYGQTECNFVL 345

Query: 380 GNFKGMKI-KPGSMGKPSPAFDVKILDENGATLPPGQEGDIALQVLPERPFGLFTHYVDN 438
            +     + K G++G+  P   V I+ E G  LP G+ G IA+   P+    +F  Y ++
Sbjct: 346 SSSAAFGVTKAGAIGRAVPGHRVAIVSEAGDELPAGESGQIAI-ASPDPV--MFLGYWND 402

Query: 439 PSKTASTLRGSFYITGDRGYMDEDGYFWFVARSDDIILSSGYRIGPFEVESALIEHPSIA 498
            + T       + +TGD G  DEDGY  F  R DD+I SSGYRIGP E+E  L  HP++ 
Sbjct: 403 AAATERKFLHGWLLTGDIGRQDEDGYVTFEGRDDDVITSSGYRIGPAEIEDCLTGHPAVQ 462

Query: 499 ESAVVSSPDPIRGEVVKAFIVLNPDYKSHDQEQLKKEIQEHVKKTTAPYKYPRKVEFIEE 558
            +A V  PD +R E+VKA+IVL+P +     E L  EI+E VK   + ++YPR+VEF+E 
Sbjct: 463 LAAAVGKPDVVRTEIVKAYIVLSPGHS--PSEALAAEIREWVKMRLSMHEYPREVEFVES 520

Query: 559 LPKTVSGKVKRNELRKK 575
           LP T +GKV R  LR+K
Sbjct: 521 LPLTTTGKVIRRLLREK 537


Lambda     K      H
   0.319    0.134    0.416 

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: 766
Number of extensions: 35
Number of successful extensions: 8
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: 580
Length of database: 550
Length adjustment: 36
Effective length of query: 544
Effective length of database: 514
Effective search space:   279616
Effective search space used:   279616
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 Apr 09 2024. 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