GapMind for Amino acid biosynthesis

 

Alignments for a candidate for CGL in Pseudomonas fluorescens FW300-N1B4

Align L-cysteine desulfidase (EC 4.4.1.28) (characterized)
to candidate Pf1N1B4_3374 Cysteine synthase (EC 2.5.1.47)

Query= BRENDA::F4K5T2
         (323 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3374
          Length = 324

 Score =  288 bits (736), Expect = 2e-82
 Identities = 162/318 (50%), Positives = 213/318 (66%), Gaps = 10/318 (3%)

Query: 10  DVTELIGNTPMVYLNKIVDGCVARIAAKLEMMEPCSSIKDRIAYSMIKDAEDKGLITPGK 69
           D    IGNTP+V +N+I    V  I AK+E   P  S+K RI  +MI DAE  G + PG 
Sbjct: 7   DNAHSIGNTPLVQINRIAPRGVT-ILAKIEGRNPGYSVKCRIGANMIWDAESTGKLKPGM 65

Query: 70  STLIEATGGNTGIGLASIGASRGYKVILLMPSTMSLERRIILRALGAEVHLTDISIGIKG 129
            T+IE T GNTGIGLA + A+RGY+++L MP++MS+ERR +L+ALGAE+ LT+ + G+KG
Sbjct: 66  -TIIEPTSGNTGIGLAFVAAARGYRLVLTMPASMSIERRKVLKALGAELVLTEPAKGMKG 124

Query: 130 QLEKAKEILSKTPGGY-IPHQFINPENPEIHYRTTGPEIWRDSAGKVDILVAGVGTGGTV 188
            +EKA EIL+  P  Y +P QF NP NP IH +TTGPEIW D+ G VD+LVAGVGTGGT+
Sbjct: 125 AIEKAAEILASDPSTYFMPGQFENPANPAIHEKTTGPEIWSDTDGAVDVLVAGVGTGGTI 184

Query: 189 TGTGKFLKE-KNKDIKVCVVEPSESAVLSGG------KPGPHLIQGIGSGEIPANLDLSI 241
           TG  +++K  + K I    VEP  S V++        KP PH IQGIG+G +P NLDLS+
Sbjct: 185 TGVSRYIKNTQGKPIISVAVEPVVSPVITQAMAGEEIKPSPHKIQGIGAGFVPKNLDLSM 244

Query: 242 VDEIIQVTGEEAIETTKLLAIKEGLLVGISSGASAAAALKVAKRPENVGKLIVVIFPSGG 301
           VD +  V+ +E+      L  +EG+L GIS GA+ A A+++A+ PE  GK IVVI P  G
Sbjct: 245 VDRVELVSDDESKAMALRLMQEEGILSGISCGAAMAVAVRLAETPEMQGKTIVVILPDSG 304

Query: 302 ERYLSTELFESVRYEAEN 319
           ERYLS+ LF  +  E EN
Sbjct: 305 ERYLSSMLFSDLFTEQEN 322


Lambda     K      H
   0.314    0.136    0.378 

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: 298
Number of extensions: 13
Number of successful extensions: 5
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: 323
Length of database: 324
Length adjustment: 28
Effective length of query: 295
Effective length of database: 296
Effective search space:    87320
Effective search space used:    87320
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: 42 (21.9 bits)
S2: 48 (23.1 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