GapMind for catabolism of small carbon sources

 

Alignments 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)



>NCBI__GCF_000009985.1:WP_011384974.1
          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 (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