GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapE in Sinorhizobium meliloti 1021

Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase; EC 3.5.1.18 (characterized)
to candidate SMc02852 SMc02852 hypothetical protein

Query= SwissProt::Q9JYL2
         (381 letters)



>FitnessBrowser__Smeli:SMc02852
          Length = 464

 Score = 75.9 bits (185), Expect = 2e-18
 Identities = 109/437 (24%), Positives = 169/437 (38%), Gaps = 83/437 (18%)

Query: 5   QSLELAKELISRPSVTPDDR---DCQKLLAERLHKIGFAAEELHFGDTKNIWL------R 55
           QSLE   +L+   S++ D     +C+K     + ++G    E    DT    +       
Sbjct: 18  QSLERLFDLVRIKSISTDPAFKAECRKAAEWLVAELGTLGFEASVRDTPGHPMVVAHHAA 77

Query: 56  RGTKAPVVCFAGHTDVVPTGPVEKWDSPPFEPAERD---GR--LYGRGAADMKTSIACFV 110
               AP + F GH DV P  P+  W++PPFEP+ R+   GR  + GRG AD K  +  FV
Sbjct: 78  GKADAPHLLFYGHYDVQPVDPLNLWETPPFEPSLREVEPGRKIITGRGTADDKGQLMTFV 137

Query: 111 TACERFVAKHPNHQGSIALLITSDEEGDALDGTTKVVDVLKAR--DELIDYCIVGEPTAV 168
            A    V  +   +G +   IT   EG+   G+  +   L+A   +   DY +V + +  
Sbjct: 138 EA----VRAYKEARGVLPCRITILFEGEEESGSPSLKPFLEANAGELKADYALVCDTSMW 193

Query: 169 DKLGDMIKNGRRGSLSGNLTVKG--KQGHIAY-PHLAINPVHTFA--------------- 210
           D+    I  G RG +   + VK   +  H  Y    A NP+H  A               
Sbjct: 194 DRETPAISAGLRGLVGEEVVVKAADRDLHSGYFGGAAANPIHILAEILAGLHDETGRVTL 253

Query: 211 ----------PALLELTQEVWDEGNEYF-----------------------PPTSFQISN 237
                     PA ++ T E   +  E F                        PT+ +I+ 
Sbjct: 254 DDFYEGVEETPAEIKATWETLGQTAEKFLGEIGLSIPSGERGRSVLELTWARPTA-EING 312

Query: 238 ING---GTGATNVIPGELNVKFNFRFSTESTEAGLKQRVHA-ILDKHGVQYDLQWSCSGQ 293
           I G   G G   VI  E + K +FR   +   A +++   A +  K      +++   G 
Sbjct: 313 ITGGYTGEGFKTVIAAEASAKVSFRLVGKQDPARIRESFRAYVRSKIPADCSIEFHAHGG 372

Query: 294 P---FLTQAGKLTDVARAAIAETCGIEAELSTTGGTSD--GRFIKAIAQE--LIELGPSN 346
                L     L   A+AA+++     A +   GG+    G F + +  E  L+  G S+
Sbjct: 373 SPAIHLPYDSALLTTAKAALSDEWPKPAVVIGMGGSIPIVGDFQRMLGMESLLVGFGLSD 432

Query: 347 ATIHQINENVRLNDIPK 363
             IH  NE   L    K
Sbjct: 433 DRIHSPNEKYELTSFHK 449


Lambda     K      H
   0.317    0.135    0.400 

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: 420
Number of extensions: 23
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 381
Length of database: 464
Length adjustment: 32
Effective length of query: 349
Effective length of database: 432
Effective search space:   150768
Effective search space used:   150768
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 (21.6 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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