Alignments for a candidate for nbaE in Marinicella litoralis KMM 3900

GapMind for catabolism of small carbon sources

Alignments for a candidate for nbaE in Marinicella litoralis KMM 3900

Align 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized)
to candidate WP_099017976.1 CCS90_RS02790 aldehyde dehydrogenase family protein

Query= SwissProt::Q9H2A2
         (487 letters)



>NCBI__GCF_002591915.1:WP_099017976.1
          Length = 787

 Score =  318 bits (814), Expect = 6e-91
 Identities = 173/479 (36%), Positives = 273/479 (56%), Gaps = 21/479 (4%)

Query: 10  LENFIDGKFLPCSSYIDSYDPSTGEVYCRVPNSGKDEIEAAVKAAREAFPSWSSRSPQER 69
           + +FI+G +    ++  S +P++GE   +V  + K+ +  AVKAA +A P W + S   R
Sbjct: 33  MSHFINGDWHSGKNHFASNNPASGERLAQVSQADKNTVNQAVKAAEKALPGWQALSGHAR 92

Query: 70  SRVLNQVADLLEQSLEEFAQAESKDQGKTLALARTMDIPRSVQNFRFFASSSLHHTSECT 129
           S  L  +A L++++   FA  E+ D GK +  +R +D+P ++++F        HH     
Sbjct: 93  SEYLYAIARLIQKNSRLFAVLETLDNGKPIRESRDIDVPLAIRHF-------YHHAGWAQ 145

Query: 130 QMDHLGCMHYTVRAPVGVAGLISPWNLPLYLLTWKIAPAMAAGNTVIAKPSELTSVTAWM 189
            +D      +     +GV G I PWN PL +L WKIAPA+A GNT++ KP+E TS+TA +
Sbjct: 146 LLD----TEFPDHEAIGVVGQIIPWNFPLLMLAWKIAPALATGNTIVIKPAEFTSLTALL 201

Query: 190 LCKLLDKAGVPPGVVNIVFGTGPRVGEALVSHPEVPLISFTGSQPTAERITQLSAPHCKK 249
             ++  +AG+P GV+N+V G G   G+ +V HP++  I+FTGS      I Q +A   KK
Sbjct: 202 FAEICQQAGLPKGVLNVVTGDGS-TGQHIVEHPDIKKIAFTGSTAVGRWIRQATAGSGKK 260

Query: 250 LSLELGGKNPAIIFEDANLDECIPATVRSSFANQGEICLCTSRIFVQKSIYSEFLKRFVE 309
           LSLELGGK+  I+  DA+LD  +   V + + NQG++C   SR+ VQ+++   F K+ + 
Sbjct: 261 LSLELGGKSAFIVCADADLDAAVEGVVDAIWFNQGQVCCAGSRLLVQEAVAERFHKKLIS 320

Query: 310 ATRKWKVGIPSDPLVSIGALISKAHLEKVRSYVKRALAEGAQIWCGEGVDKLSLPARNQA 369
              K ++G P D  + +GA+I     +K+ S V+  +  GA +          LP+   +
Sbjct: 321 RMHKLRIGDPLDKSIDMGAIIDPRQQQKIASLVQAGVDAGACL----NQSTAELPS---S 373

Query: 370 GYFMLPTVITDIKDESCCMTEEIFGPVTCVVPFDSEEEVIERANNVKYGLAATVWSSNVG 429
           G F  PT++TD+      + +EIFGPV   + F +  E +  ANN +YGLAA++WS N+ 
Sbjct: 374 GCFYPPTLLTDVSPSDQVVQDEIFGPVLVSMTFRTPSEAVALANNSRYGLAASIWSENIN 433

Query: 430 RVHRVAKKLQSGLVWTNCWLIRELNLPFGGMKSSGIGREGAKDS-YDFFT-EIKTITVK 486
               +A  +Q+G+VW NC  + +    FGG+K SG GREG K+  Y++ T +I T T K
Sbjct: 434 MAMHLAPLVQAGIVWINCTNMMDAAAGFGGVKESGFGREGGKEGLYEYLTLKINTKTQK 492



 Score = 69.7 bits (169), Expect = 4e-16
 Identities = 63/243 (25%), Positives = 108/243 (44%), Gaps = 17/243 (6%)

Query: 13  FIDGKFL-PCSSYIDSYDPSTGEVYCRVPNSGKDEIEAAVKAAREAFPSWSSRSPQERSR 71
           +I GK + P   Y  +   S G++        + ++  AV+AA  +  SWS  +  +R +
Sbjct: 519 YIGGKQVRPDGGYSYAIHNSKGQIITHAGLGNRKDVRNAVEAAATSH-SWSHMNAYQRQQ 577

Query: 72  VLNQVADLLEQSLEEFAQ-----AESKDQGKTLALARTMDIPRSVQNFRFFASSSLHHTS 126
           V+  +A+ L     EFA        SK Q +T       ++  S+Q   ++A+       
Sbjct: 578 VMYFMAENLSYRKAEFATRLESFGHSKKQAET-------EVESSIQRLSYYAAWCDKFDG 630

Query: 127 ECTQMDHLGCMHYTVRAPVGVAGLISPWNLPLYLLTWKIAPAMAAGNTVIAKPSELTSVT 186
           +   +   G +   +  P+GV  +  P   PL      +APA+A GN V+   SE   ++
Sbjct: 631 QIHSVPMRGVV-MAMHEPIGVIAIQCPDEAPLLSFISLLAPAIAMGNRVVMTASEAFPLS 689

Query: 187 AWMLCKLLDKAGVPPGVVNIVFGTGPRVGEALVSHPEVPLISFTGSQPTAERITQLSAPH 246
           A    ++L+ + VP G VNI+ G    + + L  H  V  I   GS   A+ +   SA +
Sbjct: 690 ALDFYQVLNTSDVPAGTVNIISGNRLELTKPLAGHMNVDAIWAFGSD--AQWVEHESATN 747

Query: 247 CKK 249
            K+
Sbjct: 748 LKR 750


Lambda     K      H
   0.319    0.133    0.404 

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: 865
Number of extensions: 41
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 487
Length of database: 787
Length adjustment: 37
Effective length of query: 450
Effective length of database: 750
Effective search space:   337500
Effective search space used:   337500
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: 53 (25.0 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources