GapMind for catabolism of small carbon sources

 

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

Align succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79) (characterized)
to candidate 5210745 Shew_3173 succinic semialdehyde dehydrogenase (RefSeq)

Query= BRENDA::P25526
         (482 letters)



>FitnessBrowser__PV4:5210745
          Length = 485

 Score =  584 bits (1506), Expect = e-171
 Identities = 284/480 (59%), Positives = 357/480 (74%), Gaps = 3/480 (0%)

Query: 3   LNDSNLFRQQALINGEWLDANNGEAIDVTNPANGDKLGSVPKMGADETRAAIDAANRALP 62
           + D+ L +  + I+G W      +  DV NPA+ + +  V     D+T+ AI AA RALP
Sbjct: 4   IKDTQLIKLSSYIDGRWTVGE--QRFDVVNPASQEVIAQVVDASLDDTQEAILAAKRALP 61

Query: 63  AWRALTAKERATILRNWFNLMMEHQDDLARLMTLEQGKPLAEAKGEISYAASFIEWFAEE 122
            W   +A ERA ++R WFNLMMEHQ+DL RL+TLEQGKPLAEAKGEI+Y A+FI+WFAEE
Sbjct: 62  EWSKRSANERAALMRKWFNLMMEHQEDLGRLLTLEQGKPLAEAKGEIAYGAAFIDWFAEE 121

Query: 123 GKRIYGDTIPGHQADKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKPA 182
           GKR+YGDTIP    DKR++VIKQP+GV A+ITPWNFP AMI RKA  ALAAGCT V +P+
Sbjct: 122 GKRVYGDTIPAPANDKRILVIKQPVGVVASITPWNFPNAMIARKAAAALAAGCTFVARPS 181

Query: 183 SQTPFSALALAELAIRAGVPAGVFNVVTGS-AGAVGNELTSNPLVRKLSFTGSTEIGRQL 241
             TP SALA+AELA RAG+PAGVFN+V G  A  +G  LT +P V K +FTGST +G+ L
Sbjct: 182 PLTPLSALAMAELAERAGIPAGVFNIVVGEDAVGMGKVLTQHPDVAKFTFTGSTAVGKIL 241

Query: 242 MEQCAKDIKKVSLELGGNAPFIVFDDADLDKAVEGALASKFRNAGQTCVCANRLYVQDGV 301
           + QCA  +KKVS+ELGGNAPFIVFDDAD+D AV+GAL SK+RNAGQTCVC NR++VQ GV
Sbjct: 242 LAQCATSVKKVSMELGGNAPFIVFDDADIDAAVQGALISKYRNAGQTCVCTNRIFVQKGV 301

Query: 302 YDRFAEKLQQAVSKLHIGDGLDNGVTIGPLIDEKAVAKVEEHIADALEKGARVVCGGKAH 361
              F EK   AV+ L +GDGL +GVT+GP+I + AV  V + + D +  GA++V GG+  
Sbjct: 302 AAAFTEKFTAAVANLKLGDGLGDGVTVGPMISKDAVQNVLKLVDDTVASGAKLVTGGQPS 361

Query: 362 ERGGNFFQPTILVDVPANAKVSKEETFGPLAPLFRFKDEADVIAQANDTEFGLAAYFYAR 421
           E G +F  P I+ DV     +++ E FGP+ P+  F  EA+ +A ANDTE+GLAAYFYAR
Sbjct: 362 ELGESFLAPVIVTDVTNEMPLARNEIFGPVTPIISFDSEAEALAMANDTEYGLAAYFYAR 421

Query: 422 DLSRVFRVGEALEYGIVGINTGIISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYMCIG 481
           D+ R+FRV E LEYG+VG+N GIISN  APFGG+K SG GREGSKYG++DYLEIKY+C+G
Sbjct: 422 DIGRIFRVAEGLEYGMVGVNEGIISNAAAPFGGVKQSGNGREGSKYGLDDYLEIKYLCLG 481


Lambda     K      H
   0.318    0.135    0.395 

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: 703
Number of extensions: 21
Number of successful extensions: 2
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: 482
Length of database: 485
Length adjustment: 34
Effective length of query: 448
Effective length of database: 451
Effective search space:   202048
Effective search space used:   202048
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 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