GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nbaF in Klebsiella michiganensis M5al

Align 2-amino-5-chloromuconic acid deaminase; 2-aminomuconate deaminase; EC 3.5.99.5 (characterized)
to candidate BWI76_RS07545 BWI76_RS07545 amidase

Query= SwissProt::Q38M35
         (462 letters)



>FitnessBrowser__Koxy:BWI76_RS07545
          Length = 394

 Score =  133 bits (335), Expect = 9e-36
 Identities = 119/386 (30%), Positives = 180/386 (46%), Gaps = 36/386 (9%)

Query: 69  GPLMGLPVSVKDLYGVPGLPVFAGSDE--ALPEAWQAAGPLVARLQRQLGIVVGKTHTVE 126
           GPL GL  +VKDL+ V G P   G+    AL        P+V  L       +GKTHT E
Sbjct: 22  GPLSGLTFAVKDLFDVAGYPTGGGNPHLLALSGIKNRTAPVVQTLLNNGARFIGKTHTSE 81

Query: 127 FAFGGLGVNAHWGTPRNPWSPHEHRVPGGSSAGAGVSLVQGSALLALGTDTAGSVRVPAS 186
            A+   G N H+GTPRN  +P+   +PGGSS+G+  ++       ALGTDT GSVR PAS
Sbjct: 82  LAYSMSGHNVHYGTPRNGAAPNH--IPGGSSSGSASAVSNEVCDFALGTDTGGSVRTPAS 139

Query: 187 MTGQVGLKTTVGRWPVEGIVPLSSSLDTAGVLTRTVEDLAYAFAALDTESQGLPAPAPVR 246
             G  GL+ T GR  ++G  PL +++DT G   R+ E  +   A L  + +         
Sbjct: 140 YCGLFGLRPTHGRLSLDGCQPLCATMDTCGFFARSPEVFSAVAACLFADER-------AD 192

Query: 247 VQGLRVGVPTNHFWDDIDPSIAAAVEAAVQRLAQAGAQV--VRFPLPHCEEAFDIFRRGG 304
           + G+R+      F   +      A++   QRLA+    V  +  PLP  ++ +  FR+  
Sbjct: 193 LSGVRLACHDGLF-SRLPLRSQQALQPVRQRLARFFGAVTPLAAPLPDVDDIYLAFRQ-- 249

Query: 305 LAASELAAYLDQHFPHKVERLDPVVRDRVRWAEQVSSVEYLRRKAVLQRCGAGA---ARL 361
           +   E      +       +L   VR+R  W + V+  ++    A  QR    A   A+L
Sbjct: 250 IQGYEAWQAQGETIERYGLQLGSDVRERFFWGKAVTRAQF--DAACQQRVRFAAWWDAQL 307

Query: 362 FDDVDVLLTPTVPASPPRLADIGTVETYAPANMKAMRNTA-----ISNLFGWCALTMPVG 416
            D   VL+ PTVP   P L       T     ++A+R  +     IS +     +T+PV 
Sbjct: 308 GD--AVLVMPTVPDGAPLL-------TAQAEEIEAVRRLSHDLLLISVMTQRPQVTLPVA 358

Query: 417 LDANRMPVGLQLMGPPRAEARLIGIA 442
                +P+G+  +GP  ++  L+ +A
Sbjct: 359 -QTGGLPLGISFLGPRGSDRLLVELA 383


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: 455
Number of extensions: 26
Number of successful extensions: 4
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: 394
Length adjustment: 32
Effective length of query: 430
Effective length of database: 362
Effective search space:   155660
Effective search space used:   155660
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:

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