GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nbaE in Amycolatopsis halophila YIM 93223

Align 2-aminomuconic 6-semialdehyde dehydrogenase; Aminomuconate-semialdehyde dehydrogenase; EC 1.2.1.32 (characterized)
to candidate WP_034273599.1 AMYHA_RS20335 aldehyde dehydrogenase family protein

Query= SwissProt::Q9KWS5
         (491 letters)



>NCBI__GCF_000504245.1:WP_034273599.1
          Length = 496

 Score =  347 bits (890), Expect = e-100
 Identities = 199/478 (41%), Positives = 282/478 (58%), Gaps = 10/478 (2%)

Query: 7   FVDGKWVESSKTFQD---VTPIDGSVVAVVHEADRDLVDAAVKAGHRALEGE-WGRTTAA 62
           F+DG+WV+++ T      + P + + +A V EAD   VDAAV A  RA +   W  TTA 
Sbjct: 5   FIDGRWVDTTGTAPARVVLNPANAAELATVCEADEKDVDAAVAAARRAFDDSPWRATTAR 64

Query: 63  QRVDWLRRIANEMERRQQDFLDAEMADTGKPLSMAATIDIPRGIANFRNFADILATAPVD 122
           +R + LR IA  ++R ++     E  DTGK ++    +D+    + FR +A++   A  +
Sbjct: 65  ERGELLREIARLLQRDKEHLARTESLDTGKTMA-EGRVDVDDVTSVFRYYANL---ADNE 120

Query: 123 SHRLDLPDGAYALNYAARKPLGVVGVISPWNLPLLLLTWKVAPALACGNAVVVKPSEDTP 182
           + R+     A  ++    +P+GV  +I+PWN PLL ++WK+APALA GN VV+KPSE TP
Sbjct: 121 AGRVVDTGDASVISRVVHEPVGVCSLIAPWNYPLLQMSWKLAPALAAGNTVVMKPSEVTP 180

Query: 183 GTATLLAEVMEAVGIPPGVFNLVHGFGPNSAGEFISQHPDISAITFTGESKTGSTIMRAA 242
            T   L  ++E  G+P GV NLV G G N     +S HPD+  ++FTG  +TG  IM  A
Sbjct: 181 LTTIELMRLVEEAGVPAGVVNLVLGGGANVGAPMVS-HPDVDLVSFTGGLETGKKIMAMA 239

Query: 243 AEGVKPVSFELGGKNAAVIFADCDFEKMLDGMMRALFLNSGQVCLCSERVYVERPIFDRF 302
           AEGVK V+ ELGGKN  V+FAD DF+  +D  + A F +SGQVC    R+ VE  I D F
Sbjct: 240 AEGVKRVALELGGKNPNVVFADADFDTAVDYALMAAFAHSGQVCSAGSRLIVESDIHDEF 299

Query: 303 CVALAERIKALKVDWPHETDTQMGPLISSKHRDKVLSYFELARQEGATFLAGGGVPRFGD 362
              LA R  A+++    +  T+ GPL S++HRDKV  + E A+ EGA  + GG  P    
Sbjct: 300 VAELARRADAIRLGDGLDPATECGPLSSAEHRDKVERHIEEAKTEGARLVVGGHRPT-EP 358

Query: 363 ERDNGAWVEPTVIAGLSDDARVVREEIFGPICHVTPFDSESEVIRRANDTRYGLAATIWT 422
           E  +G ++ PTV A    + R+V++E+FGP+  V  FD+E E IR ANDT YGLA  +WT
Sbjct: 359 ELADGYFLRPTVFADCDREMRIVQDEVFGPVVTVERFDTEDEAIRLANDTEYGLAGAVWT 418

Query: 423 TNLSRAHRVSELMRVGISWVNTWFLRDLRTPFGGAGLSGIGREGGMHSLNFYSELTNV 480
           ++ SRA RV+  +R G  W+N +     +  +GG G SGIGRE G   L  Y E  ++
Sbjct: 419 SDASRAQRVAGALRHGTVWINDFHPYLPQAEWGGFGKSGIGRELGPSGLEEYRETKHI 476


Lambda     K      H
   0.320    0.136    0.417 

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: 650
Number of extensions: 31
Number of successful extensions: 6
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: 491
Length of database: 496
Length adjustment: 34
Effective length of query: 457
Effective length of database: 462
Effective search space:   211134
Effective search space used:   211134
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