GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Smeli:SMc04095
          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:

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