GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaZ2 in Herbaspirillum seropedicae SmR1

Align 3-oxo-5,6-dehydrosuberyl-CoA semialdehyde dehydrogenase (EC 1.2.1.91) (characterized)
to candidate HSERO_RS20635 HSERO_RS20635 aldehyde dehydrogenase

Query= reanno::BFirm:BPHYT_RS17340
         (566 letters)



>FitnessBrowser__HerbieS:HSERO_RS20635
          Length = 561

 Score =  664 bits (1714), Expect = 0.0
 Identities = 339/567 (59%), Positives = 410/567 (72%), Gaps = 8/567 (1%)

Query: 1   MTHPLFTKHEDTLQKALTAVETRGYWSPFVEMPSPKVYGETANADGEAAFKAHLNATFQL 60
           M    F +H  TL++A++A++ RGYWSP+ E PSP+ YGE A   G AA++A L   F  
Sbjct: 1   MPTDFFNRHRATLEQAVSALQQRGYWSPYNESPSPRFYGEGAAEAGRAAYEARLERPFLF 60

Query: 61  DQPSTG--ETVGAEVSPFGFPLGVRYPKAEPAALIAAAAAAQRDWRAAGPQAWIGVCLEI 118
                G    VGAEVSP+G PLG+RYP  +   L+ +   A   WR AGPQ W GV LEI
Sbjct: 61  TPEQAGGDRWVGAEVSPYGPPLGIRYPAPDLDRLLPSMQRAAASWREAGPQVWAGVALEI 120

Query: 119 LARVNRASFEIGYSVMHTTGQAFMMAFQAGGPHAQDRALEAVVYAWDQLRRIPGDTHWEK 178
           + R+N  SFEI ++V HTTGQAF MAFQAGGPHAQDRALEA+  AW QL+ IP +  WEK
Sbjct: 121 VQRLNARSFEIAHAVQHTTGQAFTMAFQAGGPHAQDRALEAIACAWQQLQLIPAEARWEK 180

Query: 179 PQGKNPPLAMHKRYTVVPRGTGLVLGCCTFPTWNGYPGLFADLATGNTVIVKPHPGAILP 238
           PQGK+ PL M K + +VPRG GLV+GCCTFPTWN YPGLFA+LATGN VIVKPHPGAILP
Sbjct: 181 PQGKHAPLVMRKTWRIVPRGIGLVIGCCTFPTWNSYPGLFANLATGNAVIVKPHPGAILP 240

Query: 239 LALTVRIARDVLREAGFDPNVVTLLATEPNDGALVQDLALRPEIKLIDFTGSTQNGTWLE 298
           LA+TV++AR+VL EAGF P+VVTL A + +D  L + LALR EI LIDFTGS+ NG WLE
Sbjct: 241 LAITVQVAREVLAEAGFAPDVVTLAAHDASDTGLARTLALRHEIGLIDFTGSSANGDWLE 300

Query: 299 RNAHQAQVYTEKAGVNQIVIDSVDDIKAAARNVAFSLALYSGQMCTAPQNIYVPRGGIRT 358
             A QA+V TEK+G+NQI+IDS D++    +N+A SLALYSGQMCT PQNIY+PR G+RT
Sbjct: 301 ERARQARVLTEKSGINQIIIDSTDNLAGMVQNIALSLALYSGQMCTTPQNIYIPRDGVRT 360

Query: 359 AEGTLSFDEVAQAIAGAVQKLVADPARAVELLGAIQNEGVTQRIDEAAKLGRVLVESLTL 418
            +G LSF EV+QAI  AV  L  D A+AVELLGAIQNE V QRI+ A   G+VL+ES  L
Sbjct: 361 PQGQLSFVEVSQAIVQAVAHLTTDSAKAVELLGAIQNEAVLQRIELARGKGQVLLESTAL 420

Query: 419 EHPAFAGARVRTPLVLQLDAATDHAQFTKEWFGPISFVIATDSTAQSLDLAGAIASEHGA 478
            HP F GARVRTPLV+    A  +   T+E+FGPISF++  D TA ++ LA  IA++ GA
Sbjct: 421 VHPQFPGARVRTPLVM---LARRNEAITEEYFGPISFIVPVDDTATAIALAQRIATDQGA 477

Query: 479 LTLSVYSTDEAVLDDAHEASIRGGVALSINLTGGVFVNQSAAFSDFHGTGANPAANAALA 538
           LTLS Y+TD  +      A+   GVALS+NLTGGV VNQSAAFSD+HGTGANPAAN  L 
Sbjct: 478 LTLSAYTTDATLRQGLQHAAADAGVALSLNLTGGVLVNQSAAFSDYHGTGANPAANCTLT 537

Query: 539 DAAFVANRFRVVQSRVHVEPKAAPAVA 565
           DA FVA R+RVVQ+R   EP A+   A
Sbjct: 538 DADFVAARYRVVQTR---EPVASTTTA 561


Lambda     K      H
   0.318    0.133    0.394 

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: 872
Number of extensions: 23
Number of successful extensions: 3
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: 566
Length of database: 561
Length adjustment: 36
Effective length of query: 530
Effective length of database: 525
Effective search space:   278250
Effective search space used:   278250
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: 53 (25.0 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