Alignments for a candidate for aldA in Mesorhizobium ciceri WSM1271

GapMind for catabolism of small carbon sources

Alignments for a candidate for aldA in Mesorhizobium ciceri WSM1271

Align rhamnulose-1-phosphate aldolase (EC 4.1.2.19) / lactaldehyde dehydrogenase (EC 1.2.1.22) (characterized)
to candidate YP_004144317.1 Mesci_5168 class II aldolase/adducin family protein

Query= reanno::Dino:3609047
         (700 letters)



>NCBI__GCF_000185905.1:YP_004144317.1
          Length = 684

 Score =  341 bits (874), Expect = 8e-98
 Identities = 236/709 (33%), Positives = 370/709 (52%), Gaps = 43/709 (6%)

Query: 10  LESRWDDEVA---------KGMSES-ELLLYRSNILGADKRVTNYGGGNTSAKVMEADPL 59
           +++ W+DE A         KG+     L +Y + +LG + R+  +GGGNTS K    D L
Sbjct: 1   MKNLWNDEAAEKLVADYAKKGVGRDLALRVYTTRLLGGEPRLVLHGGGNTSCKTTATD-L 59

Query: 60  TGAQVEVLWVKGSGGDIGSIKMDGFATLYMDKLRALKGLYRGVAFEDEMVSYLPHCTFRL 119
            G Q +VL VKGSG D+G I+  G   + +  L   + L R +A ED +     +     
Sbjct: 60  VGDQWDVLCVKGSGWDMGVIEPQGLPAVKLKPLLKARALNR-LADEDMVALQRVNLIDPS 118

Query: 120 NPRAASIDTPLHAYVPRKHVDHVHADAIIAIAASDNSKELTQEIFGNRIGWLPWKRPGFE 179
           +P   S++T LHA++P K VDH H+ AI+AI   ++SK L + +FG+++G++P+  PGF+
Sbjct: 119 SPNP-SVETLLHAFLPHKFVDHTHSTAILAIVDQEDSKPLVKTVFGSKMGYVPYIMPGFD 177

Query: 180 LGLWLEKFCRENPEADGVVLESHGLFTWADTAKECYDQTIDVINVATRWLAERSAGVPAF 239
           L          +P+ +G++L+ HG+FT+ D AK+ YD+ I  +NVA  ++A  ++G P  
Sbjct: 178 LAKAAADIFDADPDVEGLILDKHGIFTFGDDAKQAYDRMIHYVNVAEDYIA--ASGKPK- 234

Query: 240 GGAIHESLPAAARREVAARLMPAIRGFVSDNQ------HMVGHFNDSDAVLEFVNARDME 293
             A   +LP  A+    A + P +RG V+  +       MV  F  S  +++F+N+ ++ 
Sbjct: 235 --AAKAALP--AKLATPASIAPMLRGAVAVARGEGRFDRMVSDFRTSPVIVDFINSAEIA 290

Query: 294 ALAALGTSCPDHFLRTKIRPLVVPFDPAQNNILAVLSELPDQVAAYREAYAAYYAR--CK 351
             A  G S PD  +R K  P+ +P  P  +      + +   V A+ + Y AY+      
Sbjct: 291 DYAGRGVSTPDLSIRIKTGPMALP-APDADKAGDYKAVIKSHVDAFAKDYRAYFETNDAL 349

Query: 352 HDDSPALRDPNAVVYLVPGVGMITFAKDKATARISGEFYVNAINVMRGASAVSTYQGLPE 411
            D    + D    + LVPG+GM    +    A+I+ +     I  +RGA AV  +  L +
Sbjct: 350 DDVKRTMLDQMPRLTLVPGLGMFGHGRTLKDAKIASDVGEMWIEAVRGAEAVGRFHPLSK 409

Query: 412 QEAFDIEYWLLEEAKLQRMPKPKSLAGRVALVTGGAGGIGAATAERFLAEGACVVLADIN 471
            + F +EYW LE+AKL    KPK L G+V L+TGGAG IGAATA+ F   GA  V+ D++
Sbjct: 410 ADLFPLEYWSLEQAKL-ASNKPKPLTGQVVLITGGAGAIGAATAKLFADNGAHAVVVDLD 468

Query: 472 EDSLASTQERLSERFGADVVRSVVMNVTREEAVAAAFAEASVEFGGVDILVSNAGIASSA 531
            +  A      +++ G + +  V  ++T    V AAF +A   FGGVDILVSNAG A   
Sbjct: 469 AEKAADA----AKKAGNNSI-GVAADITDPAQVRAAFDKAVAVFGGVDILVSNAGAAWEG 523

Query: 532 PIEETSLALWNKNMDILSTGYFLVSRAAFKLMRVQDMGGAVVFVASKNGLAASPNAAAYC 591
            I E   AL  K+ ++    +  V++ A ++M  Q  GG ++F  SK  +   P   AY 
Sbjct: 524 RIGELDDALLRKSFELNFFAHQSVAQNAVRIMLEQGTGGVLLFNTSKQAVNPGPKFGAYG 583

Query: 592 TAKASEIHLARCLALEGAEAGIRVNVVNPDAVLRGSKIWEGDWLEQRAGTYGTDKDGLEE 651
             KA+ + L+R  AL+    GIR N VN D +  G  +     +  R+G  G      E+
Sbjct: 584 VPKAATLFLSRQYALDYGAHGIRSNAVNADRIRSG--LLTDAMIASRSGARGVS----EK 637

Query: 652 MYRQRSLLKRSVLPEDIAEACYFFAADASSKSTGNIINVDAGNVQAFTR 700
            Y   +LL + V  +D+A+A  F     + ++T ++  VD GN+ A  R
Sbjct: 638 DYMSGNLLGQEVTAQDVAQA--FLHHALADRTTADVTTVDGGNIAAALR 684


Lambda     K      H
   0.318    0.133    0.391 

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: 902
Number of extensions: 40
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: 700
Length of database: 684
Length adjustment: 39
Effective length of query: 661
Effective length of database: 645
Effective search space:   426345
Effective search space used:   426345
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: 54 (25.4 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