GapMind for catabolism of small carbon sources

 

Alignments for a candidate for amaB in Shewanella amazonensis SB2B

Align Alpha-aminoadipic semialdehyde dehydrogenase; Alpha-AASA dehydrogenase; Aldehyde dehydrogenase family 7 member A1; Antiquitin-1; Betaine aldehyde dehydrogenase; Delta1-piperideine-6-carboxylate dehydrogenase; P6c dehydrogenase; EC 1.2.1.31; EC 1.2.1.3; EC 1.2.1.8 (characterized)
to candidate 6938573 Sama_2676 bifunctional proline dehydrogenase/pyrroline-5-carboxylate dehydrogenase (RefSeq)

Query= SwissProt::Q64057
         (539 letters)



>FitnessBrowser__SB2B:6938573
          Length = 1058

 Score =  158 bits (399), Expect = 1e-42
 Identities = 137/461 (29%), Positives = 216/461 (46%), Gaps = 26/461 (5%)

Query: 63   GEVITTYCPANNE-PIARVRQASMKDYEETIGKAKKAWNIWADIPAPKRGEIVRKIGDAL 121
            GEV     P N    + +V  A+    E+ I  A KA+  W   P   R   ++K+ D L
Sbjct: 576  GEVRDVVSPYNTTLKVGQVAFANEATIEQAIAGADKAFASWCRTPVETRANALQKLADLL 635

Query: 122  REKIQLLGRLVSLEMGKILVEGIGEVQEYVDVCDY-AAGLSRMIGGPTLPSERPGHALME 180
             E  + L  L + E GK + +GI EV+E VD C Y A    +M+  P L     G     
Sbjct: 636  EENREELIALCTREAGKSIQDGIDEVREAVDFCRYYAVQAKKMMSKPELLPGPTGELNEL 695

Query: 181  QWNPLGLVGIITAFNFPVAVFGWNNAIALITGNVCLWKGAPTTSLVSIAVTKII--AKVL 238
                 G+   I+ +NFP+A+F    A AL TGN  + K A  T L+     ++   A + 
Sbjct: 696  FLQGRGVFVCISPWNFPLAIFLGQVAAALATGNTVIAKPAEQTCLIGFRAVQLAHEAGIP 755

Query: 239  EDNL--LPGAICSLTCGGADMGTAMARDERVNLLSFTGSTQVGKQVALMVQERFGKSL-- 294
            +D L  LPG        GA +G  +  DER+  + FTGST   K +   +  R G  +  
Sbjct: 756  KDVLQFLPGT-------GAVVGAKLTSDERIGGVCFTGSTTTAKVINRALAGRDGAIIPL 808

Query: 295  -LELGGNNAIIAFEDADLSLVLPSALFAAVGTAGQRCTTVRRLFLHESIHDEVVDRLKNA 353
              E GG NA++    +    V+   + +A  +AGQRC+ +R L+L E I + V+D LK A
Sbjct: 809  IAETGGQNAMVVDSTSQPEQVVNDVVSSAFTSAGQRCSALRVLYLQEDIAERVLDVLKGA 868

Query: 354  YSQIRVGNPWDPNILYGPLHTKQAVSMFVQAVEEAKKEGGTVVYGGKVMD--HPGNYVEP 411
              ++ +GNP       GP+    A    + A  +  K+ G +++   + +    G++V P
Sbjct: 869  MDELTLGNPGSVKTDVGPV-IDAAAKANLNAHIDHIKQVGRLIHQLSLPEGTENGHFVAP 927

Query: 412  TIVTGLVHDAPIVHKETFAPILYVFKFK--NEEEVFEWNNEVKQGLSSSIFTKDLGRIFR 469
            T V   +    ++ KE F PIL+V ++K    ++V +  N    GL+  I +++ G    
Sbjct: 928  TAVE--IDSIKVLTKENFGPILHVVRYKAAGLQKVIDDINSTGFGLTLGIHSRNEGHALE 985

Query: 470  WLGPKGSDCGIVNVNIPTSGAEIG-GAFGGEKHTGGGRESG 509
                   + G V +N    GA +G   FGG+  +G G ++G
Sbjct: 986  VADK--VNVGNVYINRNQIGAVVGVQPFGGQGLSGTGPKAG 1024


Lambda     K      H
   0.319    0.137    0.417 

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: 1173
Number of extensions: 70
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 539
Length of database: 1058
Length adjustment: 40
Effective length of query: 499
Effective length of database: 1018
Effective search space:   507982
Effective search space used:   507982
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: 55 (25.8 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