GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nbaE in Shewanella loihica PV-4

Align 2-aminomuconate 6-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate 5210745 Shew_3173 succinic semialdehyde dehydrogenase (RefSeq)

Query= metacyc::MONOMER-13361
         (500 letters)



>FitnessBrowser__PV4:5210745
          Length = 485

 Score =  294 bits (753), Expect = 4e-84
 Identities = 168/480 (35%), Positives = 257/480 (53%), Gaps = 10/480 (2%)

Query: 19  QLLNYIDGNFVTSASSFANINPVNGKLISDVFEADAKQVNEAVVAAQNALKGPWGKLSVQ 78
           +L +YIDG +      F  +NP + ++I+ V +A      EA++AA+ AL   W K S  
Sbjct: 11  KLSSYIDGRWTVGEQRFDVVNPASQEVIAQVVDASLDDTQEAILAAKRALP-EWSKRSAN 69

Query: 79  DRAALIHKIADGIQARFEEFVAAEVADTGRPVHQARTLDIPRAIANFRTFADLAKTSHTD 138
           +RAAL+ K  + +    E+       + G+P+ +A+  +I    A    FA+  K  + D
Sbjct: 70  ERAALMRKWFNLMMEHQEDLGRLLTLEQGKPLAEAKG-EIAYGAAFIDWFAEEGKRVYGD 128

Query: 139 LFEMSTSDGSGALNYTVRKPLGVIGVISPWNLPLLLFTWKVAPALACGNTVVAKPSEESP 198
                 +D    +   +++P+GV+  I+PWN P  +   K A ALA G T VA+PS  +P
Sbjct: 129 TIPAPANDKRILV---IKQPVGVVASITPWNFPNAMIARKAAAALAAGCTFVARPSPLTP 185

Query: 199 SSATLLAEVMHDAGVPPGVFNLIHGFGKDSAGEFLTQHPGISALTFTGESKTGSTIMKAV 258
            SA  +AE+   AG+P GVFN++ G      G+ LTQHP ++  TFTG +  G  ++   
Sbjct: 186 LSALAMAELAERAGIPAGVFNIVVGEDAVGMGKVLTQHPDVAKFTFTGSTAVGKILLAQC 245

Query: 259 ADGVKEVSFELGGKNAAVVFADADLDAAIEGVLRSSFTNSGQVCLCSERVYVHRSIFDEF 318
           A  VK+VS ELGG    +VF DAD+DAA++G L S + N+GQ C+C+ R++V + +   F
Sbjct: 246 ATSVKKVSMELGGNAPFIVFDDADIDAAVQGALISKYRNAGQTCVCTNRIFVQKGVAAAF 305

Query: 319 VSGLKVEAERLVVGYPDQDGVNMGPLISHGHRDKVLSYYRLAVDEGATVVTGGGVPKFND 378
                     L +G    DGV +GP+IS      VL      V  GA +VTGG   +  +
Sbjct: 306 TEKFTAAVANLKLGDGLGDGVTVGPMISKDAVQNVLKLVDDTVASGAKLVTGGQPSELGE 365

Query: 379 ERDQGAYVQPTIWTGLSDKARCVTEEIFGPVCHISPFDDEDEVINRVNDSNYGLACAIWT 438
                +++ P I T ++++      EIFGPV  I  FD E E +   ND+ YGLA   + 
Sbjct: 366 -----SFLAPVIVTDVTNEMPLARNEIFGPVTPIISFDSEAEALAMANDTEYGLAAYFYA 420

Query: 439 TNLSRAHRVSRQIHVGLVWVNTWYLRDLRTPFGGVKLSGLGREGGRFSMDFYSDIANICI 498
            ++ R  RV+  +  G+V VN   + +   PFGGVK SG GREG ++ +D Y +I  +C+
Sbjct: 421 RDIGRIFRVAEGLEYGMVGVNEGIISNAAAPFGGVKQSGNGREGSKYGLDDYLEIKYLCL 480


Lambda     K      H
   0.318    0.135    0.405 

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: 520
Number of extensions: 25
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: 500
Length of database: 485
Length adjustment: 34
Effective length of query: 466
Effective length of database: 451
Effective search space:   210166
Effective search space used:   210166
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 (21.7 bits)
S2: 52 (24.6 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