GapMind for catabolism of small carbon sources

 

Aligments for a candidate for acs in Sinorhizobium meliloti 1021

Align propionate-CoA ligase (EC 6.2.1.17) (characterized)
to candidate SMc04095 SMc04095 acyl-COA synthetase

Query= BRENDA::A0A0G2K047
         (683 letters)



>lcl|FitnessBrowser__Smeli:SMc04095 SMc04095 acyl-COA synthetase
          Length = 635

 Score =  677 bits (1747), Expect = 0.0
 Identities = 325/627 (51%), Positives = 438/627 (69%), Gaps = 6/627 (0%)

Query: 58  YKTHFAASVADPERFWGKAAEQISWYKPWTKTLENRYPPSTSWFVEGMLNICYNAIDRHI 117
           Y   +AA   DP  FW  AA  I W+K   +  E        WF +G+ N C+N +DRH+
Sbjct: 5   YSEVYAAWKTDPHGFWADAASAIDWFKRPERIFEPAGGTYGHWFPDGVTNTCHNCLDRHV 64

Query: 118 ENGQGDKIAIIYDSPVTDTKATISYKEVLEQVSKLAGVLVKQGVKKGDTVVIYMPMIPQA 177
           E G+G+++A IYDSPVT     ISY ++L  V  +A +  K GV KGD ++IYMPMIPQA
Sbjct: 65  EAGRGEQLAFIYDSPVTGRIERISYADLLADVKAMAAIYRKLGVDKGDRIIIYMPMIPQA 124

Query: 178 IYAMLACARIGAIHSLIFGGFASKELSTRIDHVKPKVVVTASFGIEPGRKVEYMPLLEEA 237
             AMLA ARIGA+HS++FGGFA+ EL+ RID  + K+VV+AS G+EPGR V Y PLL++A
Sbjct: 125 AIAMLAAARIGAVHSVVFGGFAANELAMRIDDCQAKIVVSASCGLEPGRTVAYKPLLDQA 184

Query: 238 LRIGQHKPDRLLIYNRPNMEKVPLMSGRDLDWEEEMAKA----QSHDCVPVLSEHPLYIL 293
           +    HKP R LIY R +M    ++SGRD+D+ E +A A    +   C PV S  PLY+L
Sbjct: 185 IETASHKPARCLIYQR-DMLAAEMVSGRDIDFAEALAAARDAGEEASCTPVASTDPLYVL 243

Query: 294 YTSGTTGLPKGVVRPTGGYAVMLNWTMSSIYGLKPGEVWWAASDLGWVVGHSYICYGPLL 353
           YTSGTTG PKGVVR  GG+ V L W+M   +G+  G+V+WAASD+GWVVGHSYI YGPLL
Sbjct: 244 YTSGTTGQPKGVVRDNGGHMVALRWSMEHFFGVNAGDVFWAASDIGWVVGHSYIVYGPLL 303

Query: 354 HGNTTVLYEGKPVGTPDAGAYFRVLAEHGVAALFTAPTAIRAIRQQDPGAALGKQYSLTR 413
           +G T+VL+EGKPVGTPD G Y+RV++E GVA +FTAPTA+RAIR++DP AA   +Y L+R
Sbjct: 304 NGCTSVLFEGKPVGTPDPGTYWRVISERGVAVMFTAPTALRAIRKEDPEAAHAGRYDLSR 363

Query: 414 FKTLFVAGERCDVETLEWSKKVFRVPVLDHWWQTETGSPITASCIGLGNSKTPPPGQAGK 473
           F+ L++AGER D +T+ W+++  +VPV+DHWWQTETG P+  + +GLG       G    
Sbjct: 364 FRALYLAGERADPDTIRWAERALKVPVIDHWWQTETGWPVAGNPLGLGLLPV-KYGSPAV 422

Query: 474 CVPGYNVMILDDNMQKLKARSLGNIVVKLPLPPGAFSGLWKNQEAFKHLYFEKFPGYYDT 533
            +PGY+V ++DD    ++  +LGN+V+KLPLPPG    LW     F   Y E++PG+Y T
Sbjct: 423 PLPGYDVQVVDDAGHPVETGTLGNVVIKLPLPPGCLPTLWNADHRFHAAYLEEYPGFYKT 482

Query: 534 MDAGYMDEEGYLYVMSRVDDVINVAGHRISAGAIEESVLSHGTVTDCAVVGKEDPLKGHV 593
            DAGY+DE+GY+++M+R DD+INVAGHR+S GA+EE   SH  V +CAV+G  DPLKG V
Sbjct: 483 ADAGYVDEDGYIFIMARTDDIINVAGHRLSTGAMEEVCASHPDVAECAVIGIADPLKGQV 542

Query: 594 PLALCVLKKDVNATEEQVLEEIVKHVRQSIGPVAAFRNAVFVKQLPKTRSGKIPRSTLSA 653
           P    V+  +V+   E++ +E+V  VR+ IGPVAAFR AV VK+LPKTRSGKI RST+  
Sbjct: 543 PAGFLVINANVSRETEEIEKEVVGLVRERIGPVAAFRTAVCVKRLPKTRSGKILRSTIQK 602

Query: 654 LVNGKPYKVTPTIEDPSIFGHIEEVLK 680
           +++ +P+ +  TI+DP+I   I E+L+
Sbjct: 603 IIDRQPWTMPATIDDPAILDEITELLR 629


Lambda     K      H
   0.318    0.136    0.421 

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: 1360
Number of extensions: 71
Number of successful extensions: 4
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: 683
Length of database: 635
Length adjustment: 38
Effective length of query: 645
Effective length of database: 597
Effective search space:   385065
Effective search space used:   385065
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 (21.7 bits)
S2: 54 (25.4 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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