GapMind for catabolism of small carbon sources

 

Aligments for a candidate for adh in Magnetospirillum magneticum AMB-1

Align Putative aldehyde dehydrogenase SSP0762; EC 1.2.1.3 (uncharacterized)
to candidate WP_011384974.1 AMB_RS13050 aldehyde dehydrogenase family protein

Query= curated2:Q49Z69
         (475 letters)



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

 Score =  435 bits (1118), Expect = e-126
 Identities = 227/467 (48%), Positives = 307/467 (65%), Gaps = 2/467 (0%)

Query: 8   YINGEWVESTSGETL-EVINPATEEVAGTIAKGNKEDVEKAVEAADNVYLEFRHTSVKER 66
           Y++G WV+   G  L +VINPATE+V+G +A G  +D  +A++AA   +  +  T + ER
Sbjct: 8   YVDGAWVKPAKGSRLLDVINPATEQVSGRVALGGADDAVRAIQAAAKAFPAWAATPLAER 67

Query: 67  QDLLDQIVQEYKNRKEDLIQAITDELGAPLS-VAENVHYQMGLDHFEAARDALNDFQFEE 125
            ++L ++   Y+ R +++ +AI+ E+GAPL  +A+    + GL HF+ A      + FE 
Sbjct: 68  LEILAKVTAGYERRLDEIAEAISLEMGAPLERLAKPAQARAGLGHFKTALSLAKTYAFER 127

Query: 126 RRGDDLVVKEAIGVSGLITPWNFPTNQTSLKLAAAFAAGSPVVFKPSEETPFAAIILAEI 185
           R+G  LVVKE +GV  LITPWN+P NQ + K+A A AAG  +V KPSE  P++A ILAEI
Sbjct: 128 RQGTTLVVKEPVGVVSLITPWNWPMNQIACKVAPALAAGCAMVLKPSEFAPYSARILAEI 187

Query: 186 FDKVGVPKGVFNLVNGDGQGVGNPLSEHPKVRMMSFTGSGPTGSSIMKKAAEDFKKVSLE 245
             + GVP GVFN+V GDG  +G  LS HP V M+S TGS   GSS+M++ A   KKVSLE
Sbjct: 188 IHEAGVPAGVFNMVFGDGAEIGPVLSSHPLVDMVSLTGSNLAGSSVMREGAATIKKVSLE 247

Query: 246 LGGKSPYIILDDADIDGAASAAANKVVFNTGQVCTAGTRTIVPASIKEDFLTAVKEKFSQ 305
           LGGKS  II D AD   A   A   ++ NTGQ C A +R  VPA   ++      E  +Q
Sbjct: 248 LGGKSANIICDSADFKKAIGHAVKAMMGNTGQSCNAPSRLFVPAHRLDEAEGLAAELCAQ 307

Query: 306 VKVGNPREEGTQVGPIISKKQFDQVQAYIDKGIEEGAELLYGGPGKPEGLDKGYFARPTI 365
           +KVG+P +  T +GPI + +QFD+V+  I  G+EEGA+L+ GGP +PEGLDKGYF RPT+
Sbjct: 308 IKVGDPSDPETVMGPIANGRQFDKVRRMIRTGMEEGAKLVCGGPERPEGLDKGYFVRPTV 367

Query: 366 FNNVDNSMTIAQEEIFGPVMSVITYNDLDEAIKIANDTKYGLAGYVYGSDKDTLHKVARS 425
           F+ V ++MTI +EEIFGPV+S+  Y DLD+A+  AND  YGL+GYVY  D D    VAR 
Sbjct: 368 FSRVTDAMTIMREEIFGPVLSMRGYADLDDAVAGANDCVYGLSGYVYAGDLDEARAVARR 427

Query: 426 IEAGTVEINEAGRKPDLPFGGYKQSGLGREWGDYGIEEFLEVKSIAG 472
           +  G V +N A   P  PFGG +QSG+GREWG+ G EEFLE K++ G
Sbjct: 428 LRTGMVHLNGALSHPGGPFGGIRQSGVGREWGEAGFEEFLESKTLFG 474


Lambda     K      H
   0.313    0.134    0.380 

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: 614
Number of extensions: 29
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: 475
Length of database: 479
Length adjustment: 33
Effective length of query: 442
Effective length of database: 446
Effective search space:   197132
Effective search space used:   197132
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 51 (24.3 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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