GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpE in Desulfovibrio vulgaris Hildenborough

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 206897 DVU1453 long-chain-fatty-acid--CoA ligase

Query= SwissProt::Q3UNX5
         (580 letters)



>MicrobesOnline__882:206897
          Length = 564

 Score =  205 bits (522), Expect = 3e-57
 Identities = 159/529 (30%), Positives = 253/529 (47%), Gaps = 67/529 (12%)

Query: 90  SFEELGLLSRKFANILTEACSLQRGDRVMVILPKIPEWWLANVACLRTGTVLIPGTTQLT 149
           S+ +L LL+ +FA  L  A  +  GDRV V+LP +P+  +A    L+ G  ++       
Sbjct: 47  SYAKLRLLAERFAANL-RAQGVLPGDRVSVMLPNVPQAIIAFWGLLKAGCTVVMTNPLYM 105

Query: 150 QKDILYRLQSSKAKCIITDDTLAPAVDAVAAKCENLHSKLIVSQH--------------- 194
           +K++++++  S A+ +I       A+D V  K E L  +L + +                
Sbjct: 106 EKELVHQIHDSGAEYMI-------ALDLVWPKIEPLRDRLGIRKFFITRISDALGFPLNL 158

Query: 195 ------SREG-WGNL----------KEMMKYASDSHTCVDTKHDEMMAIYFTSGTTGPPK 237
                  REG W ++          K + K        V+   + +  + +T GTTG  K
Sbjct: 159 LYRFKAKREGTWRDVPFDGETVIPWKTLFKKKEGYSAKVENPREALALLQYTGGTTGISK 218

Query: 238 MIGHTHSSFGLGLSVNGRFWLDLIASDVMWNTSDTGWAK-----SAWSSVFSPWTQGACV 292
            +  TH +    LSVN +    ++        +  G           + +  P   GA +
Sbjct: 219 GVMLTHYN----LSVNVQQIKAILGESTRMRHTFLGLMPYFHVYGLTTCLTLPTALGATI 274

Query: 293 FAHYLPRFESTSILQTLSKFPITVFCSAPTAYRMLVQN-DMSSYKFNSLKHCVSAGEPIN 351
                PR+    +L  + K   T+F  AP+ Y  L+Q  D+  +   S+K+C+S   P+ 
Sbjct: 275 IP--FPRYVPRDVLVGIDKHKPTIFPGAPSIYISLMQQKDVGEFDLKSIKYCISGSAPMP 332

Query: 352 PEVMEQWRKKTGLDIYEGYGQTET--VLICGNFKGMKIKPGSMGKPSPAFDVKILD-ENG 408
            E + ++ + TG  + EG+G TE   V       G++ KPGS+G P P  + +++D E G
Sbjct: 333 LEHIRRFHELTGAQVIEGFGLTEASPVTHLNPIHGVQ-KPGSIGVPFPDTEARVVDMEVG 391

Query: 409 AT-LPPGQEGDIALQVLPERPFGLFTHYVDNPSKTASTLRGSFYITGDRGYMDEDGYFWF 467
              LPPG+ G++ +     R   +   Y++ P +TA+TLR  +  TGD   MDEDGYF+ 
Sbjct: 392 LVPLPPGKIGELII-----RGPQVMQGYLNRPDETANTLRNGWLYTGDIATMDEDGYFFI 446

Query: 468 VARSDDIILSSGYRIGPFEVESALIEHPSIAESAVVSSPDPIRGEVVKAFIVLNPDYKSH 527
           V R  D+I+  GY + P E++  L EHP + E+  V  P   RGE++KA+IV     K  
Sbjct: 447 VDRKKDMIIVGGYNVYPREIDEVLHEHPKVKEAVTVGVPHATRGEIIKAYIVPREGVK-- 504

Query: 528 DQEQLKKEIQEHVKKTTAPYKYPRKVEFIEELPKTVSGKVKRNELRKKE 576
                K EI  H ++  A YK P++VEF  ELPKT+ GKV R  LR +E
Sbjct: 505 ---LTKAEIVAHCREQLANYKVPKQVEFRNELPKTIVGKVLRRILRAEE 550


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: 770
Number of extensions: 38
Number of successful extensions: 7
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: 564
Length adjustment: 36
Effective length of query: 544
Effective length of database: 528
Effective search space:   287232
Effective search space used:   287232
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 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