GapMind for catabolism of small carbon sources

 

Aligments for a candidate for patD in Shewanella sp. ANA-3

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate 7025944 Shewana3_3092 succinate semialdehyde dehydrogenase (RefSeq)

Query= BRENDA::P77674
         (474 letters)



>lcl|FitnessBrowser__ANA3:7025944 Shewana3_3092 succinate
           semialdehyde dehydrogenase (RefSeq)
          Length = 482

 Score =  292 bits (747), Expect = 2e-83
 Identities = 167/472 (35%), Positives = 254/472 (53%), Gaps = 4/472 (0%)

Query: 1   MQHKLLINGELVSGEG-EKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAEWGQTT 59
           ++ +  ING+    +  E   + NPATG V+  +      +  AA+ AA+AA   W   T
Sbjct: 9   LRQQCYINGQWCDAQSKETVAIANPATGAVIASVPVMGQAETQAAIAAAEAALPAWRALT 68

Query: 60  PKVRAECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLN 119
            K R   L +  +++ EN    A + +   GKPL  A   E+        +FA  A+ + 
Sbjct: 69  AKERGVKLRRWFELLNENSDDLALMMTSEQGKPLAEA-KGEVTYAASFIEWFAEEAKRVY 127

Query: 120 GLAAGEYLEGHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPSEITPL 179
           G     +      M+ + P+GV A+I PWN+P  M   K APALAAG  +V+KP+  TP 
Sbjct: 128 GDTIPGHQGDKRIMVIKQPVGVTAAITPWNFPAAMITRKAAPALAAGCTMVVKPAPQTPF 187

Query: 180 TALKLAELAKDI-FPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHIISHTAS 238
           TAL LA LA+    PAGV +++ G    +G+ +  +P VR +S TGS   G  ++   A 
Sbjct: 188 TALALAVLAERAGIPAGVFSVITGDAIGIGNEMCSNPVVRKLSFTGSTQVGIKLMEQCAP 247

Query: 239 SIKRTHMELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIYDTLVE 298
           ++K+  +ELGG AP IVFDDA+I+A VEG     Y NAGQ C  A RIY Q G+YD    
Sbjct: 248 TLKKLSLELGGNAPFIVFDDANIDAAVEGAMIAKYRNAGQTCVCANRIYVQAGVYDEFAR 307

Query: 299 KLGAAVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKRKGNGY 358
           KL  AV  LK G    E    GPL + A +E+V   +E+A + G   V+ GG+     G 
Sbjct: 308 KLSIAVGKLKVGEGIGEGVTTGPLINCAAVEKVQSHLEDALSKG-ATVVAGGKPHSLGGN 366

Query: 359 YYAPTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTKDVGRA 418
           ++ PT+L        + ++E FGP+  +  F + + V+  AND+++GLA+  + +D+   
Sbjct: 367 FFEPTVLTNVDSSMRVAREETFGPLAPLFKFTDVDDVIKQANDTEFGLAAYFYGRDISLV 426

Query: 419 HRVSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHV 470
            +V+  L+YG   VNT  +     P GG K SG G++ S +G+E+Y  ++++
Sbjct: 427 WKVTEALEYGMVGVNTGLISTEVAPFGGMKSSGLGREGSKFGIEEYLEIKYI 478


Lambda     K      H
   0.317    0.134    0.397 

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: 514
Number of extensions: 23
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: 474
Length of database: 482
Length adjustment: 34
Effective length of query: 440
Effective length of database: 448
Effective search space:   197120
Effective search space used:   197120
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: 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 preprint 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