GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nbaE in Azospirillum thiophilum BV-S

Align aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate WP_045585596.1 AL072_RS27435 aldehyde dehydrogenase family protein

Query= BRENDA::Q83XU8
         (485 letters)



>NCBI__GCF_001305595.1:WP_045585596.1
          Length = 484

 Score =  294 bits (753), Expect = 4e-84
 Identities = 173/457 (37%), Positives = 251/457 (54%), Gaps = 17/457 (3%)

Query: 25  PLNNAVIAKVHEAGRAEVDAAVAAAQAALKGAWGRMSLAQRVEVLYAVADGINRRFDDFL 84
           P      A +     A+VD AVAAA+AA   A+   S  +R+ ++  + D    R+D   
Sbjct: 35  PATEEPFATIALGTSADVDRAVAAARAAFP-AFSATSREERLALMRRLLDAYKARYDAVA 93

Query: 85  AAEVEDTGKPMSLARHVDIPRGAANFKIFADVVKNVPTEFFEMPTPDGVGAINYAVRRPV 144
                + G P +LA       G A+     + +++   E     T           + P+
Sbjct: 94  DTLSREMGAPTTLAHRSQAAMGTAHLARMIETLESFAFEELRGST--------LISKEPI 145

Query: 145 GVVGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEETPQTAALLGEVMNTAGVPPGVYN 204
           GVVG+I PWN P+  +  KV PALA G T+V+KPSE  P  A L  E ++ AGVP GV+N
Sbjct: 146 GVVGMITPWNWPINQIMCKVAPALAAGCTMVLKPSEIAPLNATLFAEAVHEAGVPKGVFN 205

Query: 205 VVHGFGPNSTGEFLTSHPDVNAITFTGETGTGEAIMKAAADGARPVSLELGGKNAAIVFA 264
           +V+G GP + GE +  HP V+ ++FTG T  G  + KAAAD  + V  ELGGK+A I+  
Sbjct: 206 LVNGDGP-TVGEAIARHPGVDMVSFTGSTRAGILVAKAAADTVKRVHQELGGKSANIILD 264

Query: 265 DCDLDKAIEGTLRSCFANCGQVCLGTERVYVERPIFDRFVSRLKKGAEGMQLGRPEDLAT 324
           D DLD+A++  + SC  N GQ C    R++V   + D+ ++  +  AE ++ G P    T
Sbjct: 265 DADLDRAVKLGVESCMNNSGQSCNAPTRMFVPASLHDQAIAIARTTAERLKAGAPAAADT 324

Query: 325 GMGPLISQEHREKVLSYYKKAVEAGATVVTGGGVPEMPEALKGGAWVQPTIWTGLGDDSV 384
            +GP++SQ   +K+    +  +  GA +VTGG  P  PE L  G +V+PT++  + DD  
Sbjct: 325 RLGPVVSQIQYDKIQRLIEAGIAEGAELVTGG--PGRPEGLNRGYYVRPTVFANVTDDMT 382

Query: 385 VAREEIFGPCALVMPFDSEEEVIRRANDNDYGLARRIWTTNLSRAHRVAGAIEVGIAWVN 444
           +AREEIFGP   ++P+ SEEE IRRAND  YGLA  + + +L RA +VA  +  G  ++N
Sbjct: 383 IAREEIFGPVLAILPYGSEEEAIRRANDTPYGLASYVQSGSLERARKVAARMRSGNVYIN 442

Query: 445 --SWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELK 479
             +W   D    FGG KQSG GRE     LE + E+K
Sbjct: 443 HPAW---DAGAPFGGYKQSGNGREYAEFGLEEFLEIK 476


Lambda     K      H
   0.318    0.135    0.406 

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: 518
Number of extensions: 19
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: 485
Length of database: 484
Length adjustment: 34
Effective length of query: 451
Effective length of database: 450
Effective search space:   202950
Effective search space used:   202950
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: 41 (21.7 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