GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpE in Methanospirillum stamsii Pt1

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_109940824.1 DLD82_RS09165 AMP-binding protein

Query= SwissProt::Q3UNX5
         (580 letters)



>NCBI__GCF_003173335.1:WP_109940824.1
          Length = 616

 Score =  528 bits (1359), Expect = e-154
 Identities = 261/552 (47%), Positives = 368/552 (66%), Gaps = 19/552 (3%)

Query: 33  NFSNYESMKQDFKIEIPEYFNFAKDVLDQWTNMEKAGKRLSNPAFWWIDGNGEELRWSFE 92
           N  +Y+   ++F+IE+PEYFNF  DV+D W   ++     +  A  W +  GEE  ++F 
Sbjct: 60  NMQSYDETYRNFRIEVPEYFNFGFDVVDAWAKKDR-----NKIAMVWTNQKGEEKFFTFR 114

Query: 93  ELGLLSRKFANILTEACSLQRGDRVMVILPKIPEWWLANVACLRTGTVLIPGTTQLTQKD 152
           ++   S +  N++ +   + +GDRV+++L ++PEWW   VA ++ G + IP  T LT KD
Sbjct: 115 DISRRSNEIVNMMIKY-KIGKGDRVLIMLHRVPEWWFMTVALIKIGAIYIPAPTMLTPKD 173

Query: 153 ILYRLQSSKAKCIITDDTLAPAVDAVAAKCENLHSKLIVSQHSREGW-GNLKEMMKYASD 211
           I YR+ +++AK +ITD   A  VD +   C  L +K++V     +GW    +E+M  A  
Sbjct: 174 IAYRVNTAEAKMVITDMENAHKVDEIVGDCPTLVTKMVVDGEC-DGWLSYTRELMYPAPV 232

Query: 212 SHTCVD------TKHDEMMAIYFTSGTTGPPKMIGHTHSSFGLGLSVNGRFWLDLIASDV 265
           S   ++      TK  E M I+F+SGTTG PKM+ H+HS + LG  V  RFW D+  +D+
Sbjct: 233 SSRIINLKGMRKTKSSEPMVIFFSSGTTGEPKMVQHSHS-YPLGHIVTARFWHDVRNNDL 291

Query: 266 MWNTSDTGWAKSAWSSVFSPWTQGACVFAH-YLPRFESTSILQTLSKFPITVFCSAPTAY 324
            +  SDTGWAKSAW  +F  W +GA +F + Y  RF +T +L  + K+ IT FC+ PT Y
Sbjct: 292 HFTVSDTGWAKSAWGKLFGQWIEGAAIFVYDYRSRFNATELLPLIEKYGITTFCAPPTIY 351

Query: 325 RMLVQNDMSSYKFNSLKHCVSAGEPINPEVMEQWRKKTGLDIYEGYGQTETVLICGNFKG 384
           RML+  D+  + F+ L+HCVSAGE INPEV++ W+  TGL+IYEGYGQTETVL  G F  
Sbjct: 352 RMLIMADLRKWDFSELRHCVSAGELINPEVIKAWKDATGLEIYEGYGQTETVLCVGTFPC 411

Query: 385 MKIKPGSMGKPSPAFDVKILDENGATLPPGQEGDIALQVLPERPFGLFTHYVDNPSKTAS 444
           M+ K GSMGKPSP +++++ DE+G  + PG+EG IA++  P RP G F  Y  N    A+
Sbjct: 412 MEPKYGSMGKPSPGWEIELHDEDGNQVKPGEEGSIAIKTEP-RPVGFFMEYWGNEEANAN 470

Query: 445 TLRGSFYITGDRGYMDEDGYFWFVARSDDIILSSGYRIGPFEVESALIEHPSIAESAVVS 504
           + +G +Y TGDR   D DGYFWFV R DD+I +SGYRIGPFEVESA+IEHP++ E+AVV 
Sbjct: 471 SFKGGYYYTGDRAMKDNDGYFWFVGRDDDVIKASGYRIGPFEVESAIIEHPAVQEAAVVG 530

Query: 505 SPDPIRGEVVKAFIVLNPDYKSHDQEQLKKEIQEHVKKTTAPYKYPRKVEFIEELPKTVS 564
           SPD IRG +VKAF+VL   ++    E++ ++IQE+VK +TAPYKYPRK+EFI+ELPKT+S
Sbjct: 531 SPDIIRGFIVKAFVVLKAGFE--PSEKISRDIQEYVKNSTAPYKYPRKIEFIKELPKTIS 588

Query: 565 GKVKRNELRKKE 576
           GK+KR +LR+ E
Sbjct: 589 GKIKRKDLRELE 600


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: 1007
Number of extensions: 46
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: 616
Length adjustment: 37
Effective length of query: 543
Effective length of database: 579
Effective search space:   314397
Effective search space used:   314397
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