GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__ANA3:7025944
          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:

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