GapMind for catabolism of small carbon sources

 

Alignments for a candidate for adh in Catellicoccus marimammalium M35/04/3

Align Putative aldehyde dehydrogenase AldA; EC 1.2.1.3 (uncharacterized)
to candidate WP_009488515.1 C683_RS01225 NADP-dependent glyceraldehyde-3-phosphate dehydrogenase

Query= curated2:Q2YV11
         (495 letters)



>NCBI__GCF_000313915.1:WP_009488515.1
          Length = 473

 Score =  235 bits (600), Expect = 2e-66
 Identities = 160/489 (32%), Positives = 266/489 (54%), Gaps = 31/489 (6%)

Query: 11  ENYGLFINGEFVKGSSDETIEVTNPATGETLSHITRAKDKDVDHAVEVAQEAFESWSLTS 70
           ++Y   +NGE+ KG+S +TI +  PATG+ L  +   ++K+++  ++ A++A + W   +
Sbjct: 2   KSYLNLVNGEW-KGTS-QTITIKEPATGKELGTVPAMEEKEIEEVMQSARQAQKEWQALA 59

Query: 71  KSERAQMLRDIGDKLMAQKDKIAMIETLNNGKPIRETTAIDIPFAARHFHYFASVIET-- 128
             ERAQ+L      L  +  +I  + +    K I ++ A  I    R     A   E   
Sbjct: 60  VVERAQILHQAAQLLKKEAVEIGTLLS----KEIAKSRAASIQEVERTADLIAYTAEEGC 115

Query: 129 -------EEGTVNDIDKDTMSIVRHEPIGVVGAVVAWNFPMLLAAWKIAPAIAAGNTIVI 181
                  E G+ +  D++ ++ V  E +GVV A+  +N+P+ LAA KIAPA+  GNT+V 
Sbjct: 116 RMEGQILEGGSFSKKDQNKIAFVHKEAMGVVLAIAPFNYPVNLAASKIAPALIGGNTVVF 175

Query: 182 QPSSSTPLSLLEVAKIFQEV-LPKGVVNILTGKGSESGNAIFNHDGVDKLSFTGSTDVGY 240
           +  +   +S L++A+IF E  +P GV+N +TG+GS  G+A+  H  VD ++FTGST++G 
Sbjct: 176 KTPTQGAISGLQLARIFHEAGVPAGVLNTVTGRGSVIGDALVTHPEVDAINFTGSTEIGT 235

Query: 241 QVAEAAAKHLVPATLELGGKSANIILDDANLDLAVEGIQLGILFNQGEVCSAGSRLLVHE 300
            +AE A   + P  +ELGGK A ++L+DA+L+ A + I  G     G+ C+A  R+ V E
Sbjct: 236 HIAELAG--MKPCIMELGGKDAALVLEDADLENAAKEIVAGAFQYSGQRCTAIKRVFVTE 293

Query: 301 KIYDQLVPRLQEAFSNIKVGDPQDEATQMGSQTGKDQLDKIQSYIDVAKESDAQILAGGH 360
           K  D LV  +Q+    + VG P++ A  +     +   D I+  I+ A      +L G  
Sbjct: 294 KNADALVAAIQKEMETLSVGLPEENA-DITPLIDRFVADHIEFLIEDA------LLKGAV 346

Query: 361 RLTENGLDKGFFFEPTLIAVPDNHHKLAQEEIFGPVLTVIKVKDDQEAIDIANDSKYGLA 420
             T+   ++   + P L+        LA EE FGPVL +++VKD +E I +AN S+YGL 
Sbjct: 347 AKTKYQRERNLIW-PMLLDQVTVDMDLAWEEPFGPVLPILRVKDVEEMIRLANASEYGLQ 405

Query: 421 GGVFSQNITRALNIAKAVRTGRIWINTYNQVPEGA---PFGGYKKSGIGRETYKGALSNY 477
             +F+ N   A+ I KA++ G + +N  ++   GA   PF G K SG+G +  K ++   
Sbjct: 406 SAIFTNNYPLAMEIGKALKVGTVHMN--HRTQRGADHFPFLGIKNSGLGVQGIKYSIDAM 463

Query: 478 QQVKNIYID 486
            ++K+   +
Sbjct: 464 MRMKSFVFE 472


Lambda     K      H
   0.315    0.133    0.377 

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: 488
Number of extensions: 34
Number of successful extensions: 6
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: 495
Length of database: 473
Length adjustment: 34
Effective length of query: 461
Effective length of database: 439
Effective search space:   202379
Effective search space used:   202379
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: 42 (22.0 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