GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pad-dh in Magnetospirillum magneticum AMB-1

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_011384974.1 AMB_RS13050 aldehyde dehydrogenase family protein

Query= BRENDA::P05091
         (517 letters)



>lcl|NCBI__GCF_000009985.1:WP_011384974.1 AMB_RS13050 aldehyde
           dehydrogenase family protein
          Length = 479

 Score =  273 bits (698), Expect = 1e-77
 Identities = 181/496 (36%), Positives = 260/496 (52%), Gaps = 36/496 (7%)

Query: 36  CNQIFINNEW-HDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWR 94
           C   +++  W   A   +    +NP+T +V  +VA G  +D  +A++AA  AF     W 
Sbjct: 4   CLDFYVDGAWVKPAKGSRLLDVINPATEQVSGRVALGGADDAVRAIQAAAKAFPA---WA 60

Query: 95  RMDASHRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWAD 154
               + R  +L ++    ER    +A   +L+ G P        L+ + K  +  AG   
Sbjct: 61  ATPLAERLEILAKVTAGYERRLDEIAEAISLEMGAP--------LERLAKPAQARAGLG- 111

Query: 155 KYHGKTIPIDGDFFSYTRH--------EPVGVCGQIIPWNFPLLMQAWKLGPALATGNVV 206
             H KT       +++ R         EPVGV   I PWN+P+   A K+ PALA G  +
Sbjct: 112 --HFKTALSLAKTYAFERRQGTTLVVKEPVGVVSLITPWNWPMNQIACKVAPALAAGCAM 169

Query: 207 VMKVAEQTPLTALYVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEI 266
           V+K +E  P +A  +A +I EAG P GV N+V G G   G  ++SH  VD V+ TGS   
Sbjct: 170 VLKPSEFAPYSARILAEIIHEAGVPAGVFNMVFGDGAEIGPVLSSHPLVDMVSLTGSNLA 229

Query: 267 GRVIQVAAGSSNLKRVTLELGGKSPNIIMSDADMDWAVEQAHFALFFNQGQCCCAGSRTF 326
           G  + +  G++ +K+V+LELGGKS NII   AD   A+  A  A+  N GQ C A SR F
Sbjct: 230 GSSV-MREGAATIKKVSLELGGKSANIICDSADFKKAIGHAVKAMMGNTGQSCNAPSRLF 288

Query: 327 VQEDIYDEFVERSVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLC 386
           V     DE    +        VG+P D +T  GP  +  QF K+   I TG +EGAKL+C
Sbjct: 289 VPAHRLDEAEGLAAELCAQIKVGDPSDPETVMGPIANGRQFDKVRRMIRTGMEEGAKLVC 348

Query: 387 GG---GIAADRGYFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYG 443
           GG       D+GYF++PTVF  V D MTI +EEIFGPV+ +  +  +++ V  AN+  YG
Sbjct: 349 GGPERPEGLDKGYFVRPTVFSRVTDAMTIMREEIFGPVLSMRGYADLDDAVAGANDCVYG 408

Query: 444 LAAAVFTKDLDKANYLSQALQAGTVWVNCYDVFGAQS----PFGGYKMSGSGRELGEYGL 499
           L+  V+  DLD+A  +++ L+ G V +N     GA S    PFGG + SG GRE GE G 
Sbjct: 409 LSGYVYAGDLDEARAVARRLRTGMVHLN-----GALSHPGGPFGGIRQSGVGREWGEAGF 463

Query: 500 QAYTEVKTVTVKVPQK 515
           + + E KT+    P++
Sbjct: 464 EEFLESKTLFGSEPKE 479


Lambda     K      H
   0.319    0.136    0.409 

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: 609
Number of extensions: 28
Number of successful extensions: 5
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: 517
Length of database: 479
Length adjustment: 34
Effective length of query: 483
Effective length of database: 445
Effective search space:   214935
Effective search space used:   214935
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 (21.8 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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