Alignments for a candidate for iolA in Marinicella litoralis KMM 3900

GapMind for catabolism of small carbon sources

Alignments for a candidate for iolA in Marinicella litoralis KMM 3900

Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_099017976.1 CCS90_RS02790 aldehyde dehydrogenase family protein

Query= BRENDA::P42412
         (487 letters)



>NCBI__GCF_002591915.1:WP_099017976.1
          Length = 787

 Score =  223 bits (568), Expect = 2e-62
 Identities = 148/474 (31%), Positives = 245/474 (51%), Gaps = 18/474 (3%)

Query: 6   KLKNYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAV 65
           K+ ++ING+W   K     +  NPA+ E L QV  + K  ++ A + A +A   W  ++ 
Sbjct: 32  KMSHFINGDWHSGKNHFASN--NPASGERLAQVSQADKNTVNQAVKAAEKALPGWQALSG 89

Query: 66  PRRARILFNFQQLLSQHKEELAHLITIENGKNTKEALG-EVGRGIENVEFAAGAPSLMMG 124
             R+  L+   +L+ ++    A L T++NGK  +E+   +V   I +    AG   L+  
Sbjct: 90  HARSEYLYAIARLIQKNSRLFAVLETLDNGKPIRESRDIDVPLAIRHFYHHAGWAQLL-- 147

Query: 125 DSLASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLL 184
                   D E  ++   IGVVG I P+NFP+++  W    A+A GNT ++KP+E T L 
Sbjct: 148 --------DTEFPDHE-AIGVVGQIIPWNFPLLMLAWKIAPALATGNTIVIKPAEFTSLT 198

Query: 185 TEKLVELFEKAGLPKGVFNVVYGAHDVVNGILEHPEIKAISFVGSKPVGEYVYKKGSENL 244
                E+ ++AGLPKGV NVV G       I+EHP+IK I+F GS  VG ++ +  + + 
Sbjct: 199 ALLFAEICQQAGLPKGVLNVVTGDGSTGQHIVEHPDIKKIAFTGSTAVGRWIRQATAGSG 258

Query: 245 KRVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMAKL 304
           K++    G K+  IV  DA+L+  V  +V A + + G+ C A + + V+E +A+ F  KL
Sbjct: 259 KKLSLELGGKSAFIVCADADLDAAVEGVVDAIWFNQGQVCCAGSRLLVQEAVAERFHKKL 318

Query: 305 QEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVSDDGYFV 364
             ++  ++IG+ LD  + +G +I    +++  S ++ G++ GA L     E +   G F 
Sbjct: 319 ISRMHKLRIGDPLDKSIDMGAIIDPRQQQKIASLVQAGVDAGACLNQSTAE-LPSSGCFY 377

Query: 365 GPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNAIRY 424
            PT+  +V+    + +DEIF PVL  +  +   EA+ +AN S +   A +++ N N   +
Sbjct: 378 PPTLLTDVSPSDQVVQDEIFGPVLVSMTFRTPSEAVALANNSRYGLAASIWSENINMAMH 437

Query: 425 FRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKKVVT 478
               + AG++ IN       A   F G K S FG     GK+ +  Y   K+ T
Sbjct: 438 LAPLVQAGIVWINC-TNMMDAAAGFGGVKESGFG--REGGKEGLYEYLTLKINT 488



 Score = 64.7 bits (156), Expect = 1e-14
 Identities = 57/240 (23%), Positives = 107/240 (44%), Gaps = 7/240 (2%)

Query: 8   KNYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAVPR 67
           K YI G+ V      Y   ++ +  +++    +  ++D+  A + AA +  +WS +   +
Sbjct: 517 KMYIGGKQVRPDGG-YSYAIHNSKGQIITHAGLGNRKDVRNAVEAAATSH-SWSHMNAYQ 574

Query: 68  RARILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLMMGDSL 127
           R ++++   + LS  K E A  +    G + K+A  EV   I+ + + A       G   
Sbjct: 575 RQQVMYFMAENLSYRKAEFATRLE-SFGHSKKQAETEVESSIQRLSYYAAWCDKFDGQIH 633

Query: 128 ASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLTEK 187
           +     V  A +  PIGV+    P   P++    +   AIA+GN  ++  SE  PL    
Sbjct: 634 SVPMRGVVMAMHE-PIGVIAIQCPDEAPLLSFISLLAPAIAMGNRVVMTASEAFPLSALD 692

Query: 188 LVELFEKAGLPKGVFNVVYGAH-DVVNGILEHPEIKAISFVGSKPVGEYVYKKGSENLKR 246
             ++   + +P G  N++ G   ++   +  H  + AI   GS    ++V  + + NLKR
Sbjct: 693 FYQVLNTSDVPAGTVNIISGNRLELTKPLAGHMNVDAIWAFGSD--AQWVEHESATNLKR 750


Lambda     K      H
   0.318    0.136    0.396 

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: 815
Number of extensions: 39
Number of successful extensions: 4
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 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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