GapMind for catabolism of small carbon sources

 

Aligments for a candidate for nbaF in Desulfovibrio vulgaris Miyazaki F

Align 2-amino-5-chloromuconic acid deaminase; 2-aminomuconate deaminase; EC 3.5.99.5 (characterized)
to candidate 8502127 DvMF_2838 aspartyl/glutamyl-tRNA amidotransferase subunit A (RefSeq)

Query= SwissProt::Q38M35
         (462 letters)



>lcl|FitnessBrowser__Miya:8502127 DvMF_2838 aspartyl/glutamyl-tRNA
           amidotransferase subunit A (RefSeq)
          Length = 501

 Score =  181 bits (460), Expect = 4e-50
 Identities = 160/483 (33%), Positives = 217/483 (44%), Gaps = 47/483 (9%)

Query: 6   LSLAEHAARLRRRELTAVALIDTCAQHHARMEPRLNAYKTWDGARARSAAAAVDTLLDQG 65
           LSLAE   RL RRELTA  +   C       EP + A     G  A + A A+D     G
Sbjct: 11  LSLAEVRDRLARRELTAEQVTAACLDRITATEPAIAALLVTRGEGALAEARALDAA---G 67

Query: 66  QDLG-PLMGLPVSVKDLYGVPGLPVFAGSDEALPEAWQAAGPLVARLQRQLGIVVGKTHT 124
            D   PL G+P++VKD     G     GS              V +L+    +++GKT+ 
Sbjct: 68  PDPAKPLWGVPLTVKDALTTAGTRTTCGSRILGDFTPHYDAFAVGKLREAGAVILGKTNM 127

Query: 125 VEFAFGGLGVNAHWGTPRNPWSPHEHRVPGGSSAGAGVSLVQGSALLALGTDTAGSVRVP 184
            EFA G    N+ +G  RNPW+    RVPGGSS G+  S+  G    +LGTDT GS+R P
Sbjct: 128 DEFAMGSSTENSAFGPTRNPWNVA--RVPGGSSGGSAASVAAGQCFGSLGTDTGGSIRQP 185

Query: 185 ASMTGQVGLKTTVGRWPVEGIVPLSSSLDTAGVLTRTVEDLAYAFAAL------DTESQG 238
           AS+ G VGLK T GR    G+V   SSLD  G LTRTVED A   + +      D  S  
Sbjct: 186 ASLCGCVGLKPTYGRVSRFGLVAYGSSLDQIGPLTRTVEDAALLLSVIAGHDPRDATSAT 245

Query: 239 LPA-------PAPVRVQGLRVGVPTNHFWDDIDPSIAAAVEAAVQRLAQAGAQVVRFPLP 291
           LP         +   + G+R+GVP     + IDP ++AA EAA+      GA +V   LP
Sbjct: 246 LPVDDYMGALASRKDLSGVRIGVPREFRGEGIDPEVSAACEAALDTARGLGATIVDVELP 305

Query: 292 H-------------CEEAFDIFR----RGGLAASELAAYLDQHFPHKVERLDPVVRDRVR 334
           H              E + ++ R    R G  A       D +   + E     V+ R+ 
Sbjct: 306 HTPYSIAAYYIIAPAEASSNLARFDGVRYGRRAESPRDLADLYVRSRAEGFGDEVQRRIM 365

Query: 335 WAEQVSSV----EYLRRKAVLQR-CGAGAARLFDDVDVLLTPTVPASPPRLADIGTVETY 389
               V S      Y R+ A ++R       +     DVL  P  P +   L ++    T 
Sbjct: 366 LGTYVLSSGYYDAYYRKAAQVRRLIREDYEKALSRCDVLCGPASPVTAWGLGEL----TS 421

Query: 390 APANMKAMRNTAIS-NLFGWCALTMPVGLDA-NRMPVGLQLMGPPRAEARLIGIALGIEA 447
            P  M  M    +S NL G   L +PVG+ + + MPVGLQ++G    E  L+  A  +  
Sbjct: 422 DPLKMYMMDVFTLSLNLAGLPGLCIPVGMGSRSGMPVGLQMLGRAFGEGDLLAAANVLSG 481

Query: 448 LIG 450
            +G
Sbjct: 482 ALG 484


Lambda     K      H
   0.320    0.135    0.411 

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: 523
Number of extensions: 25
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: 462
Length of database: 501
Length adjustment: 34
Effective length of query: 428
Effective length of database: 467
Effective search space:   199876
Effective search space used:   199876
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 (21.8 bits)
S2: 51 (24.3 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