GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nbaF in Rhodanobacter denitrificans 2APBS1

Align 2-amino-5-chloromuconic acid deaminase; 2-aminomuconate deaminase; EC 3.5.99.5 (characterized)
to candidate WP_015447086.1 R2APBS1_RS04915 amidase

Query= SwissProt::Q38M35
         (462 letters)



>NCBI__GCF_000230695.2:WP_015447086.1
          Length = 537

 Score =  119 bits (297), Expect = 3e-31
 Identities = 149/496 (30%), Positives = 217/496 (43%), Gaps = 65/496 (13%)

Query: 4   AHLSLAEHAARLRRRELTAVALIDTCAQHHARMEPRLNAYKTWDGARARSAAAAVDTLLD 63
           A L     A  L  R+LT  AL+D   Q   R  P L A        A + A A+DT   
Sbjct: 36  AQLQQRMDAGTLDSRQLTQ-ALLDRI-QRIDRSGPTLRAVIE-SNPEALALAGALDTKRT 92

Query: 64  QGQDLGPLMGLPVSVKDLYGVPGLPVFAGSDEALPEAW--QAAGPLVARLQRQLGIVVGK 121
           +    GPL G+PV +KD        +      AL +A   + AG LV RL++   +V+GK
Sbjct: 93  KAH--GPLYGIPVLLKDNIDTGDRMLTTAGSLALIDAPAPRDAG-LVERLRKAGALVLGK 149

Query: 122 THTVEFA-----FGGLGVNAHWGTPRNPWSPHEHRVPGGSSAGAGVSLVQGSALLALGTD 176
           T+  E+A         G +   G  +NP+     R P GSSAG+  ++  G A  A+G++
Sbjct: 150 TNLSEWANFRSNHASSGWSGRGGQTKNPYVLD--RNPCGSSAGSAAAVAAGLATAAIGSE 207

Query: 177 TAGSVRVPASMTGQVGLKTTVGRWPVEGIVPLSSSLDTAGVLTRTVEDLAYAFAALDTES 236
           T GS+  PA+M G VG+K T+G     GIVP+S S DTAG + R+V D A     +    
Sbjct: 208 TDGSIICPAAMNGIVGIKPTLGLVSRSGIVPISHSQDTAGPMARSVADAAALLTVIAGSD 267

Query: 237 QGLPAPA--------------PVRVQGLRVGVPTNHFWDDIDPSIAAAVEAAVQRLAQAG 282
              PA A              P  ++G R+GV         +P+    +E A+  +   G
Sbjct: 268 PRDPATAEADRHATDYTKFLDPNGLRGKRIGVVRQ--LAGAEPNADRVLEQAIALMKAQG 325

Query: 283 AQVV-RFPLPHCEEAFD-----------------IFRRGGLAASELAAYLDQHFPHKVER 324
           A +V    LPH  E  +                 +  R GL A  LA  +  +  H  E 
Sbjct: 326 AIIVDPVKLPHLAELGEPEMTVLLYDFKHDIDAYLANRRGLKARTLADLVAFNQAHAGEE 385

Query: 325 LDPVVRDRVRWAEQ---VSSVEYLRRKAVLQRC----GAGAARLFDDVDVLLTPT-VPA- 375
           +    ++    AE+   +S   Y    A  +R     G  AA     +D LL P+  PA 
Sbjct: 386 MPWFGQELFEQAEKKGPLSDKAYTDALAKAKRLSGPEGIDAALQAQHLDALLAPSWGPAF 445

Query: 376 -SPPRLADIGTVETYAPANMKAMRNTAISNLFGWCALTMPVGLDANRMPVGLQLMGPPRA 434
            + P L D   + +  P    A +  A++   G+ ++T+P G  A+ +PVG+ L G   +
Sbjct: 446 MTDPVLGD--HIVSGDPTVGGASQPAAVA---GYPSITVPAGF-AHGLPVGIVLFGAKWS 499

Query: 435 EARLIGIALGIEALIG 450
           E  LI IA G E   G
Sbjct: 500 EPALISIAYGFEQHAG 515


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: 585
Number of extensions: 32
Number of successful extensions: 3
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: 537
Length adjustment: 34
Effective length of query: 428
Effective length of database: 503
Effective search space:   215284
Effective search space used:   215284
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: 52 (24.6 bits)

This GapMind analysis is from Sep 24 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