GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolA in Psychromonas ingrahamii 37

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_011770382.1 PING_RS10720 betaine-aldehyde dehydrogenase

Query= BRENDA::P42412
         (487 letters)



>NCBI__GCF_000015285.1:WP_011770382.1
          Length = 488

 Score =  261 bits (668), Expect = 3e-74
 Identities = 169/482 (35%), Positives = 255/482 (52%), Gaps = 10/482 (2%)

Query: 1   MAEIRKLKNYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTW 60
           M+ +   +NYI+G+++ + T +  +V+NPAT +V   V  + +     A ++A   F TW
Sbjct: 1   MSSLVVYQNYIHGQYIPNDTGETFEVINPATGQVSYLVETADQAVQQAAIESAKSGFATW 60

Query: 61  SKVAVPRRARILFNFQQLLSQHKEELAHLITIENGKNTKEA-LGEVGRGIENVEFAAGAP 119
           SK+    R+RIL     LL +H +ELA    ++ GK  +EA + +V  G + +EF AG  
Sbjct: 61  SKMTPIERSRILLKAVALLREHNDELAVGEVLDTGKPWQEASVVDVVTGTDTIEFFAGLA 120

Query: 120 SLMMGDSLASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSE 179
             + G+    +  D      R P+G+  GI  +N+P+ + CW    A+A GN  I KPSE
Sbjct: 121 PSIEGNQ-QQVGDDFYYTR-REPLGICAGIGAWNYPLQIACWKAAPALACGNVMIFKPSE 178

Query: 180 RTPLLTEKLVELFEKAGLPKGVFNVVYGAHDVVNGILEHPEIKAISFVGSKPVGEYVYKK 239
            TP    +L E+F  AG+P GVFNVV G   V   +  H +I  +SF G    G+ V   
Sbjct: 179 ETPRGAMRLAEIFTLAGVPDGVFNVVQGDGRVGAWLTGHEDIAKVSFTGEVGTGKKVMAA 238

Query: 240 GSENLKRVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADE 299
            + +LK V    G K+  I+ NDA+LE+ V+  +   F + GE C     V V+E I   
Sbjct: 239 AAGSLKAVTMELGGKSPLIIFNDADLENAVSAAMLGNFYTQGEVCTNGTRVFVQEEIYPR 298

Query: 300 FMAKLQEKV-ADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRE--- 355
           F+ +L E+   +I  G+ +D     GP+I +D++++ L YI  G  EGA L+  G++   
Sbjct: 299 FIKRLVERTEQNIICGDPMDPETNFGPLISKDHQQKVLDYITIGKAEGATLLTGGKKLHP 358

Query: 356 NVSDDGYFVGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLF 415
             + DGYFV PTIF + T EMT+ K+EIF PV+SV+   +  E +  AN +     A LF
Sbjct: 359 ENAPDGYFVAPTIFTDCTDEMTLTKEEIFGPVMSVLTFSDEDEVVRRANDTRLGLAAGLF 418

Query: 416 TSNSNAIRYFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKK 475
           T +          IDAG+  IN    +P A  P  G+K S  G    NG +++  YT+ K
Sbjct: 419 TQDITRAHRVIHQIDAGICWINSFGASP-AEMPVGGYKMS--GVGRENGSETLKSYTQIK 475

Query: 476 VV 477
            V
Sbjct: 476 AV 477


Lambda     K      H
   0.318    0.136    0.396 

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: 587
Number of extensions: 31
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: 487
Length of database: 488
Length adjustment: 34
Effective length of query: 453
Effective length of database: 454
Effective search space:   205662
Effective search space used:   205662
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 24 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